Sender: LSF System <lsf@node1419>
Subject: Job 4390670: <iteration_215347> Done

Job <iteration_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347> was used as the working directory.
Started at Wed Oct 24 16:38:56 2012
Results reported at Wed Oct 24 16:38:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
echo starting
ls iteration*/exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo some scatter or gather jobs failed;
echo ${return_code} > exited;
exit 1;
fi
ls exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo previous iteration failed;
echo ${return_code} > exited;
exit 1;
fi
/xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 215347 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
return_code=$?
if [ ${return_code} -ne 0 ]; then
echo iterator failed ${return_code};
echo ${return_code} > exited;
exit ${return_code};
fi
cat iteration1/jobSubmissions.txt >> jobSubmissions.txt
rm -f iteration1/jobSubmissions.txt
echo '*** Scatter Gather stdandard out:' 2>&1
cat iteration1/scatter-gather.out.txt 2>&1
rm -f iteration1/scatter-gather.out.txt 2>&1
echo '*** Scatter Gather stdandard err:' 2>&1
cat iteration1/scatter-gather.err.txt 2>&1
rm -f iteration1/scatter-gather.err.txt 2>&1
ls iteration1/sg-next-iteration.txt 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
rm -f iteration1/sg-next-iteration.txt
else
rm -f scatterGatherParameters.txt
rm -f programParameters.txt
mv iteration1/* /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347
rmdir iteration*
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :      0.65 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

starting
ls: iteration*/exited: No such file or directory
ls: exited: No such file or directory
Running scatter-gather-iterator with the following args: /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 215347 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
Finished in 1 iterations
*** Scatter Gather stdandard out:
Sender: LSF System <lsf@node1701>
Subject: Job 4390664: <gather_215347> Done

Job <gather_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1701>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1> was used as the working directory.
Started at Wed Oct 24 15:22:48 2012
Results reported at Wed Oct 24 16:38:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
ls scatter.*/exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo some scatter jobs failed;
echo ${return_code} > exited;
exit 1;
fi
if [ `ls -1 scatter.*/success | wc -l` -ne 229 ]; then
echo expected result files missing, try rerunning;
echo 1 > exited;
exit 1;
fi
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/run_matlab.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ fh_MutSigCoverageGather "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/" "LUAD" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUAD/1910307/0.MutSigPreprocess.Finished/LUAD.maf" "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "4" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUAD/1910307/0.MutSigPreprocess.Finished/LUAD.patients.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
echo gather failed;
echo ${return_code} > exited;
exit ${return_code};
fi
rm -f prepareResults.out
echo '*** Prepare stdandard out:' 2>&1
cat prepare.out 2>&1
rm -f prepare.out 2>&1
echo '*** Prepare stdandard err:' 2>&1
cat prepare.err 2>&1
rm -f prepare.err 2>&1
echo '*** Scatter stdandard out:' 2>&1
cat scatter.*/scatter.out 2>&1
rm -f scatter.*/scatter.out 2>&1
echo '*** Scatter stdandard err:' 2>&1
cat scatter.*/scatter.err 2>&1
rm -f scatter.*/scatter.err 2>&1
echo '*** Scatter retry log:'
head scatter.*.tries
echo
rm -f scatter.*.tries
rm -f scatter.*/success
rmdir scatter.*
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :   2911.26 sec.
    Max Memory :      7730 MB
    Max Swap   :      8602 MB

    Max Processes  :         8
    Max Threads    :        54

The output (if any) follows:

ls: scatter.*/exited: No such file or directory
Warning: No display specified.  You will not be able to display graphics on the screen.
fh_MutSigCoverageGather
100/229 200/229 
229 files found
100/229 200/229 
229 files found
100/229 200/229 
229 files found
Creating summed FWB coverage file: ./LUAD.summed_coverage.fwb
Loading target file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Opening files: 10/229 20/229 30/229 40/229 50/229 60/229 70/229 80/229 90/229 100/229 110/229 120/229 130/229 140/229 150/229 160/229 170/229 180/229 190/229 200/229 210/229 220/229 
Summing and writing output file:
1/4283949 Elapsed time is 0.013884 seconds.
100001/4283949 Elapsed time is 11.695621 seconds.
200001/4283949 Elapsed time is 23.623105 seconds.
300001/4283949 Elapsed time is 24.073128 seconds.
400001/4283949 Elapsed time is 24.496351 seconds.
500001/4283949 Elapsed time is 24.948021 seconds.
600001/4283949 Elapsed time is 25.347667 seconds.
700001/4283949 Elapsed time is 25.763250 seconds.
800001/4283949 Elapsed time is 26.179226 seconds.
900001/4283949 Elapsed time is 26.594344 seconds.
1000001/4283949 Elapsed time is 32.193979 seconds.
1100001/4283949 Elapsed time is 32.622002 seconds.
1200001/4283949 Elapsed time is 33.042331 seconds.
1300001/4283949 Elapsed time is 33.471559 seconds.
1400001/4283949 Elapsed time is 33.882458 seconds.
1500001/4283949 Elapsed time is 34.287021 seconds.
1600001/4283949 Elapsed time is 34.695114 seconds.
1700001/4283949 Elapsed time is 35.103900 seconds.
1800001/4283949 Elapsed time is 35.506656 seconds.
1900001/4283949 Elapsed time is 35.924599 seconds.
2000001/4283949 Elapsed time is 36.321737 seconds.
2100001/4283949 Elapsed time is 36.745658 seconds.
2200001/4283949 Elapsed time is 37.150326 seconds.
2300001/4283949 Elapsed time is 37.554083 seconds.
2400001/4283949 Elapsed time is 37.967218 seconds.
2500001/4283949 Elapsed time is 38.374075 seconds.
2600001/4283949 Elapsed time is 38.791624 seconds.
2700001/4283949 Elapsed time is 39.207350 seconds.
2800001/4283949 Elapsed time is 39.618175 seconds.
2900001/4283949 Elapsed time is 40.031917 seconds.
3000001/4283949 Elapsed time is 40.437461 seconds.
3100001/4283949 Elapsed time is 40.851761 seconds.
3200001/4283949 Elapsed time is 41.253089 seconds.
3300001/4283949 Elapsed time is 41.664127 seconds.
3400001/4283949 Elapsed time is 42.077340 seconds.
3500001/4283949 Elapsed time is 42.489831 seconds.
3600001/4283949 Elapsed time is 42.890933 seconds.
3700001/4283949 Elapsed time is 44.066024 seconds.
3800001/4283949 Elapsed time is 44.469570 seconds.
3900001/4283949 Elapsed time is 44.877677 seconds.
4000001/4283949 Elapsed time is 45.291141 seconds.
4100001/4283949 Elapsed time is 45.692116 seconds.
4200001/4283949 Elapsed time is 46.096045 seconds.

Closing input files
Done
Getting covered territory tally... 1931/193094 3862/193094 5793/193094 7724/193094 9655/193094 11586/193094 13517/193094 15448/193094 17379/193094 19310/193094 21241/193094 23172/193094 25103/193094 27034/193094 28965/193094 30896/193094 32827/193094 34758/193094 36689/193094 38620/193094 40551/193094 42482/193094 44413/193094 46344/193094 48275/193094 50206/193094 52137/193094 54068/193094 55999/193094 57930/193094 59861/193094 61792/193094 63723/193094 65654/193094 67585/193094 69516/193094 71447/193094 73378/193094 75309/193094 77240/193094 79171/193094 81102/193094 83033/193094 84964/193094 86895/193094 88826/193094 90757/193094 92688/193094 94619/193094 96550/193094 98481/193094 100412/193094 102343/193094 104274/193094 106205/193094 108136/193094 110067/193094 111998/193094 113929/193094 115860/193094 117791/193094 119722/193094 121653/193094 123584/193094 125515/193094 127446/193094 129377/193094 131308/193094 133239/193094 135170/193094 137101/193094 139032/193094 140963/193094 142894/193094 144825/193094 146756/193094 148687/193094 150618/193094 152549/193094 154480/193094 156411/193094 158342/193094 160273/193094 162204/193094 164135/193094 166066/193094 167997/193094 169928/193094 171859/193094 173790/193094 175721/193094 177652/193094 179583/193094 181514/193094 183445/193094 185376/193094 187307/193094 189238/193094 191169/193094 
k=1
                      mut   n 90536 N 20590434240  rate 4.40e-06 (1.00x)  ci 4.37e-06 to 4.43e-06

k=2
                   C->mut   n 75309 N 10495996992  rate 7.18e-06 (1.63x)  ci 7.12e-06 to 7.23e-06
                   A->mut   n 15227 N 10094437248  rate 1.51e-06 (0.34x)  ci 1.48e-06 to 1.53e-06

k=3
                     C->A   n 46125 N 3498665664  rate 1.32e-05 (3.00x)  ci 1.31e-05 to 1.33e-05
                 C->(T/G)   n 29184 N 6997331328  rate 4.17e-06 (0.95x)  ci 4.12e-06 to 4.22e-06
                   A->mut   n 15227 N 10094437248  rate 1.51e-06 (0.34x)  ci 1.48e-06 to 1.53e-06

k=4
                  *CpG->A   n 15609 N  380670135  rate 4.10e-05 (9.33x)  ci 4.04e-05 to 4.17e-05
            *Cp(A/C/T)->A   n 30516 N 3117995529  rate 9.79e-06 (2.23x)  ci 9.68e-06 to 9.90e-06
                 C->(T/G)   n 29184 N 6997331328  rate 4.17e-06 (0.95x)  ci 4.12e-06 to 4.22e-06
                   A->mut   n 15227 N 10094437248  rate 1.51e-06 (0.34x)  ci 1.48e-06 to 1.53e-06

Saving ./LUAD.mutcategs.txt
all files are *.bin: will read in BINARY MODE
100/229 200/229 
229 files found
Loading target file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Collapsing targets to genes...
10000/193094 20000/193094 30000/193094 40000/193094 50000/193094 60000/193094 70000/193094 80000/193094 90000/193094 100000/193094 110000/193094 120000/193094 130000/193094 140000/193094 150000/193094 160000/193094 170000/193094 180000/193094 190000/193094 
Note: total territory is 120724948: appears to include noncoding areas
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Saving ./LUAD.coverage.mat
Deleting intermediate files
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1
mFile: fh_MutSigCoverageGather
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/fh_MutSigCoverageGather /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ LUAD /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUAD/1910307/0.MutSigPreprocess.Finished/LUAD.maf /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt /xchip/cga1/annotation/db/tracks/hg19/c65e hg19 /xchip/cga1/annotation/db/ucsc/hg19 4 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUAD/1910307/0.MutSigPreprocess.Finished/LUAD.patients.txt
*** Prepare stdandard out:
cat: prepare.out: No such file or directory
*** Prepare stdandard err:
cat: prepare.err: No such file or directory
*** Scatter stdandard out:
Sender: LSF System <lsf@node1421>
Subject: Job 4388201: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1421>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000001> was used as the working directory.
Started at Wed Oct 24 15:01:19 2012
Results reported at Wed Oct 24 15:01:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000001.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000001.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4244-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4244-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4244-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000001.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.29 sec.
    Max Memory :      4720 MB
    Max Swap   :      5522 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4244-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4244-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4244-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4244-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4388205: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000002> was used as the working directory.
Started at Wed Oct 24 15:01:24 2012
Results reported at Wed Oct 24 15:01:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000002.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000002.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4249-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4249-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4249-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000002.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.72 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4249-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4249-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4249-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4249-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1729>
Subject: Job 4388210: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1729>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000003> was used as the working directory.
Started at Wed Oct 24 15:01:24 2012
Results reported at Wed Oct 24 15:01:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000003.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000003.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4250-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4250-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4250-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000003.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.99 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4250-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4250-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4250-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4250-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4388219: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000004> was used as the working directory.
Started at Wed Oct 24 15:01:24 2012
Results reported at Wed Oct 24 15:01:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000004.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000004.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4382-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4382-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4382-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000004.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.55 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4382-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4382-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4382-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4382-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1427>
Subject: Job 4388225: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1427>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000005> was used as the working directory.
Started at Wed Oct 24 15:01:31 2012
Results reported at Wed Oct 24 15:02:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000005.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000005.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4384-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4384-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4384-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000005.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.78 sec.
    Max Memory :      4727 MB
    Max Swap   :      5467 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4384-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4384-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4384-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4384-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1418>
Subject: Job 4388232: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1418>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000006> was used as the working directory.
Started at Wed Oct 24 15:01:40 2012
Results reported at Wed Oct 24 15:02:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000006.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000006.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4389-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4389-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4389-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000006.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     34.26 sec.
    Max Memory :      4718 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4389-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4389-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4389-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4389-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4388238: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000007> was used as the working directory.
Started at Wed Oct 24 15:01:40 2012
Results reported at Wed Oct 24 15:02:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000007.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000007.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4390-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4390-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4390-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000007.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.09 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4390-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4390-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4390-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4390-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1549>
Subject: Job 4388243: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1549>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000008> was used as the working directory.
Started at Wed Oct 24 15:01:40 2012
Results reported at Wed Oct 24 15:02:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000008.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000008.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4395-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4395-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4395-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000008.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.08 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4395-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4395-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4395-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4395-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1546>
Subject: Job 4388249: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000009> was used as the working directory.
Started at Wed Oct 24 15:01:40 2012
Results reported at Wed Oct 24 15:02:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000009.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000009.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4396-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4396-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4396-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000009.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.49 sec.
    Max Memory :      4717 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4396-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4396-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4396-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4396-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4388255: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000010> was used as the working directory.
Started at Wed Oct 24 15:01:40 2012
Results reported at Wed Oct 24 15:02:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000010.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000010.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4397-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4397-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4397-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000010.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.38 sec.
    Max Memory :         7 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4397-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4397-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4397-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4397-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1543>
Subject: Job 4388259: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1543>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000011> was used as the working directory.
Started at Wed Oct 24 15:01:45 2012
Results reported at Wed Oct 24 15:02:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000011.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000011.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4398-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4398-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4398-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000011.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.29 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4398-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4398-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4398-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4398-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4388265: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000012> was used as the working directory.
Started at Wed Oct 24 15:01:40 2012
Results reported at Wed Oct 24 15:02:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000012.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000012.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4402-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4402-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4402-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000012.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.90 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4402-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4402-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4402-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4402-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1542>
Subject: Job 4388273: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1542>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000013> was used as the working directory.
Started at Wed Oct 24 15:01:46 2012
Results reported at Wed Oct 24 15:02:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000013.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000013.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4403-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4403-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4403-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000013.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.10 sec.
    Max Memory :      4686 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4403-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4403-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4403-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4403-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 4388281: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000014> was used as the working directory.
Started at Wed Oct 24 15:01:46 2012
Results reported at Wed Oct 24 15:02:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000014.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000014.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4405-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4405-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4405-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000014.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.89 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4405-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4405-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4405-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4405-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4388288: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000015> was used as the working directory.
Started at Wed Oct 24 15:01:46 2012
Results reported at Wed Oct 24 15:02:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000015.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000015.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4410-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4410-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4410-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000015.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.34 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4410-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4410-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4410-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4410-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1706>
Subject: Job 4388292: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1706>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000016> was used as the working directory.
Started at Wed Oct 24 15:01:55 2012
Results reported at Wed Oct 24 15:02:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000016.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000016.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4415-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4415-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4415-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000016.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.62 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4415-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4415-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4415-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4415-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1431>
Subject: Job 4388299: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1431>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000017> was used as the working directory.
Started at Wed Oct 24 15:01:55 2012
Results reported at Wed Oct 24 15:02:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000017.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000017.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4417-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4417-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4417-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000017.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.31 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4417-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4417-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4417-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4417-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1554>
Subject: Job 4388309: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000018> was used as the working directory.
Started at Wed Oct 24 15:02:12 2012
Results reported at Wed Oct 24 15:08:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000018.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000018.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4418-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4418-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4418-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000018.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     67.43 sec.
    Max Memory :      4656 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4418-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4418-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4418-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4418-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4388340: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000019> was used as the working directory.
Started at Wed Oct 24 15:02:15 2012
Results reported at Wed Oct 24 15:02:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000019.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000019.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4420-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4420-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4420-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000019.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     22.15 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4420-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4420-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4420-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4420-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4388348: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000020> was used as the working directory.
Started at Wed Oct 24 15:02:15 2012
Results reported at Wed Oct 24 15:02:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000020.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000020.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4422-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4422-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4422-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000020.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.94 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4422-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4422-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4422-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4422-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1645>
Subject: Job 4388358: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000021> was used as the working directory.
Started at Wed Oct 24 15:02:15 2012
Results reported at Wed Oct 24 15:02:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000021.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000021.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4424-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4424-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4424-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000021.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     22.25 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4424-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4424-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4424-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4424-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4388370: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000022> was used as the working directory.
Started at Wed Oct 24 15:02:15 2012
Results reported at Wed Oct 24 15:02:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000022.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000022.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4425-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4425-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4425-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000022.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.07 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4425-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4425-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4425-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4425-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1424>
Subject: Job 4388381: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1424>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000023> was used as the working directory.
Started at Wed Oct 24 15:02:15 2012
Results reported at Wed Oct 24 15:02:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000023.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000023.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4426-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4426-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4426-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000023.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.07 sec.
    Max Memory :      4724 MB
    Max Swap   :      5465 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4426-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4426-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4426-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4426-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4388393: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000024> was used as the working directory.
Started at Wed Oct 24 15:02:15 2012
Results reported at Wed Oct 24 15:02:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000024.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000024.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4427-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4427-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4427-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000024.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.31 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4427-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4427-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4427-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4427-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4388403: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000025> was used as the working directory.
Started at Wed Oct 24 15:02:15 2012
Results reported at Wed Oct 24 15:02:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000025.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000025.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4430-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4430-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4430-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000025.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.01 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4430-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4430-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4430-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4430-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 4388467: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000026> was used as the working directory.
Started at Wed Oct 24 15:02:15 2012
Results reported at Wed Oct 24 15:02:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000026.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000026.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4432-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4432-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4432-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000026.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.74 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4432-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4432-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4432-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4432-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 4388484: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000027> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000027.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000027.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4433-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4433-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4433-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000027.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.77 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4433-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4433-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4433-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4433-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4388495: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000028> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000028.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000028.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-4434-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-4434-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4434-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000028.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.45 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-4434-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-4434-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-4434-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-4434-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1707>
Subject: Job 4388509: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1707>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000029> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000029.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000029.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-5420-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-5420-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5420-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000029.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.44 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5420-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-5420-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-5420-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-5420-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4388526: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000030> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000030.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000030.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-5423-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-5423-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5423-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000030.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.36 sec.
    Max Memory :         5 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5423-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-5423-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-5423-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-5423-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 4388536: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000031> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000031.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000031.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-5425-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-5425-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5425-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000031.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.77 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5425-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-5425-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-5425-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-5425-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4388548: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000032> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000032.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000032.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-5428-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-5428-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5428-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000032.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.00 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5428-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-5428-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-5428-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-5428-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1644>
Subject: Job 4388560: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000033> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000033.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000033.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-5429-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-5429-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5429-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000033.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.26 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5429-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-5429-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-5429-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-5429-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1654>
Subject: Job 4388605: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1654>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000034> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000034.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000034.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-05-5715-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-05-5715-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5715-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000034.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.16 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-05-5715-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-05-5715-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-05-5715-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-05-5715-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4388612: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000035> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000035.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000035.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z000-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z000-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z000-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000035.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.85 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z000-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z000-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z000-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z000-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1699>
Subject: Job 4388619: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000036> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000036.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000036.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z001-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z001-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z001-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000036.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.69 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z001-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z001-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z001-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z001-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 4388697: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000037> was used as the working directory.
Started at Wed Oct 24 15:02:25 2012
Results reported at Wed Oct 24 15:02:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000037.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000037.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z003-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z003-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z003-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000037.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.38 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z003-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z003-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z003-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z003-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1545>
Subject: Job 4388707: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1545>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000038> was used as the working directory.
Started at Wed Oct 24 15:02:28 2012
Results reported at Wed Oct 24 15:02:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000038.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000038.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z004-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z004-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z004-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000038.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.51 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z004-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z004-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z004-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z004-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1546>
Subject: Job 4388715: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000039> was used as the working directory.
Started at Wed Oct 24 15:02:36 2012
Results reported at Wed Oct 24 15:03:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000039.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000039.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z005-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z005-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z005-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000039.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.86 sec.
    Max Memory :      4695 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z005-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z005-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z005-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z005-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4388733: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000040> was used as the working directory.
Started at Wed Oct 24 15:02:36 2012
Results reported at Wed Oct 24 15:02:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000040.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000040.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z007-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z007-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z007-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000040.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.58 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z007-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z007-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z007-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z007-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4388742: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000041> was used as the working directory.
Started at Wed Oct 24 15:02:36 2012
Results reported at Wed Oct 24 15:02:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000041.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000041.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z008-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z008-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z008-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000041.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.89 sec.
    Max Memory :         7 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z008-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z008-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z008-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z008-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1531>
Subject: Job 4388758: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000042> was used as the working directory.
Started at Wed Oct 24 15:02:36 2012
Results reported at Wed Oct 24 15:03:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000042.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000042.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z009-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z009-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z009-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000042.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.89 sec.
    Max Memory :      4727 MB
    Max Swap   :      5466 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z009-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z009-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z009-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z009-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1540>
Subject: Job 4388764: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1540>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000043> was used as the working directory.
Started at Wed Oct 24 15:02:36 2012
Results reported at Wed Oct 24 15:03:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000043.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000043.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z010-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z010-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z010-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000043.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.59 sec.
    Max Memory :      4718 MB
    Max Swap   :      5459 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z010-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z010-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z010-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z010-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1543>
Subject: Job 4388772: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1543>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000044> was used as the working directory.
Started at Wed Oct 24 15:02:46 2012
Results reported at Wed Oct 24 15:03:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000044.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000044.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z011-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z011-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z011-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000044.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.89 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z011-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z011-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z011-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z011-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4388780: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000045> was used as the working directory.
Started at Wed Oct 24 15:02:48 2012
Results reported at Wed Oct 24 15:03:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000045.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000045.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z012-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z012-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z012-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000045.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.01 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z012-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z012-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z012-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z012-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1536>
Subject: Job 4388836: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1536>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000046> was used as the working directory.
Started at Wed Oct 24 15:02:56 2012
Results reported at Wed Oct 24 15:03:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000046.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000046.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z013-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z013-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z013-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000046.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.48 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z013-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z013-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z013-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z013-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4388843: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000047> was used as the working directory.
Started at Wed Oct 24 15:03:16 2012
Results reported at Wed Oct 24 15:03:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000047.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000047.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z014-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z014-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z014-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000047.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.12 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z014-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z014-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z014-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z014-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4388849: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000048> was used as the working directory.
Started at Wed Oct 24 15:03:16 2012
Results reported at Wed Oct 24 15:03:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000048.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000048.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z015-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z015-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z015-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000048.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.00 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z015-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z015-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z015-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z015-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1703>
Subject: Job 4388854: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1703>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000049> was used as the working directory.
Started at Wed Oct 24 15:03:16 2012
Results reported at Wed Oct 24 15:03:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000049.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000049.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z016-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z016-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z016-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000049.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.03 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z016-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z016-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z016-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z016-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1702>
Subject: Job 4388859: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000050> was used as the working directory.
Started at Wed Oct 24 15:03:16 2012
Results reported at Wed Oct 24 15:03:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000050.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000050.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z017-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z017-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z017-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000050.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.77 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z017-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z017-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z017-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z017-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 4388865: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000051> was used as the working directory.
Started at Wed Oct 24 15:03:16 2012
Results reported at Wed Oct 24 15:03:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000051.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000051.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z018-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z018-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z018-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000051.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.10 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z018-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z018-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z018-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z018-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4388872: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000052> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000052.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000052.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z020-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z020-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z020-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000052.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.83 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z020-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z020-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z020-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z020-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 4388877: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000053> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000053.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000053.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z021-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z021-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z021-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000053.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.13 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z021-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z021-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z021-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z021-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 4388883: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000054> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000054.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000054.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z022-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z022-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z022-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000054.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.48 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z022-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z022-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z022-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z022-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1699>
Subject: Job 4388891: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000055> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000055.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000055.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z023-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z023-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z023-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000055.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.09 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z023-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z023-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z023-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z023-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1644>
Subject: Job 4388898: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000056> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000056.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000056.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z025-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z025-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z025-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000056.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.42 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z025-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z025-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z025-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z025-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4388905: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000057> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000057.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000057.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z026-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z026-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z026-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000057.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.42 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z026-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z026-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z026-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z026-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1726>
Subject: Job 4388911: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000058> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000058.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000058.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z027-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z027-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z027-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000058.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.93 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z027-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z027-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z027-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z027-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4388917: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000059> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000059.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000059.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z028-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z028-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z028-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000059.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.93 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z028-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z028-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z028-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z028-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4388923: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000060> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000060.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000060.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z030-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z030-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z030-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000060.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.08 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z030-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z030-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z030-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z030-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4388933: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000061> was used as the working directory.
Started at Wed Oct 24 15:03:25 2012
Results reported at Wed Oct 24 15:03:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000061.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000061.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z031-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z031-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z031-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000061.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.16 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z031-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z031-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z031-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z031-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1422>
Subject: Job 4388942: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1422>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000062> was used as the working directory.
Started at Wed Oct 24 15:03:27 2012
Results reported at Wed Oct 24 15:20:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000062.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000062.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z032-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z032-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z032-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000062.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     91.59 sec.
    Max Memory :      4720 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z032-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z032-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z032-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z032-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1546>
Subject: Job 4388957: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000063> was used as the working directory.
Started at Wed Oct 24 15:03:36 2012
Results reported at Wed Oct 24 15:04:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000063.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000063.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z033-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z033-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z033-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000063.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.99 sec.
    Max Memory :      4719 MB
    Max Swap   :      5461 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z033-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z033-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z033-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z033-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1531>
Subject: Job 4388970: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000064> was used as the working directory.
Started at Wed Oct 24 15:03:36 2012
Results reported at Wed Oct 24 15:04:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000064.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000064.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z035-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z035-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z035-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000064.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.70 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z035-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z035-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z035-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z035-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1540>
Subject: Job 4388981: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1540>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000065> was used as the working directory.
Started at Wed Oct 24 15:03:36 2012
Results reported at Wed Oct 24 15:04:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000065.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000065.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z036-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z036-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z036-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000065.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.61 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z036-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z036-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z036-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z036-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4388990: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000066> was used as the working directory.
Started at Wed Oct 24 15:03:36 2012
Results reported at Wed Oct 24 15:04:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000066.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000066.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z037-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z037-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z037-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000066.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.46 sec.
    Max Memory :      4709 MB
    Max Swap   :      5467 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z037-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z037-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z037-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z037-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4389002: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000067> was used as the working directory.
Started at Wed Oct 24 15:03:48 2012
Results reported at Wed Oct 24 15:04:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000067.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000067.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z038-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z038-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z038-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000067.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.56 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z038-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z038-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z038-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z038-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1528>
Subject: Job 4389009: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1528>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000068> was used as the working directory.
Started at Wed Oct 24 15:03:50 2012
Results reported at Wed Oct 24 15:04:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000068.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000068.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z039-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z039-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z039-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000068.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.66 sec.
    Max Memory :      4724 MB
    Max Swap   :      5461 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z039-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z039-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z039-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z039-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 4389021: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000069> was used as the working directory.
Started at Wed Oct 24 15:04:05 2012
Results reported at Wed Oct 24 15:04:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000069.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000069.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z040-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z040-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z040-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000069.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.23 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z040-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z040-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z040-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z040-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4389031: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000070> was used as the working directory.
Started at Wed Oct 24 15:04:16 2012
Results reported at Wed Oct 24 15:04:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000070.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000070.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z041-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z041-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z041-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000070.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.41 sec.
    Max Memory :        10 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z041-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z041-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z041-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z041-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1702>
Subject: Job 4389041: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000071> was used as the working directory.
Started at Wed Oct 24 15:04:16 2012
Results reported at Wed Oct 24 15:04:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000071.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000071.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z042-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z042-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z042-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000071.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.16 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z042-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z042-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z042-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z042-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1424>
Subject: Job 4389051: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1424>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000072> was used as the working directory.
Started at Wed Oct 24 15:04:16 2012
Results reported at Wed Oct 24 15:04:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000072.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000072.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z043-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z043-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z043-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000072.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.10 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z043-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z043-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z043-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z043-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4389115: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000073> was used as the working directory.
Started at Wed Oct 24 15:04:25 2012
Results reported at Wed Oct 24 15:04:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000073.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000073.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z044-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z044-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z044-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000073.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.32 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z044-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z044-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z044-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z044-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 4389122: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000074> was used as the working directory.
Started at Wed Oct 24 15:04:25 2012
Results reported at Wed Oct 24 15:04:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000074.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000074.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z045-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z045-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z045-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000074.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.60 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z045-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z045-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z045-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z045-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4389133: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000075> was used as the working directory.
Started at Wed Oct 24 15:04:25 2012
Results reported at Wed Oct 24 15:04:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000075.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000075.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z046-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z046-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z046-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000075.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.42 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z046-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z046-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z046-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z046-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4389144: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000076> was used as the working directory.
Started at Wed Oct 24 15:04:25 2012
Results reported at Wed Oct 24 15:04:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000076.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000076.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z047-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z047-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z047-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000076.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.11 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z047-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z047-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z047-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z047-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1422>
Subject: Job 4389154: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1422>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000077> was used as the working directory.
Started at Wed Oct 24 15:04:27 2012
Results reported at Wed Oct 24 15:20:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000077.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000077.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z048-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z048-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z048-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000077.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     85.43 sec.
    Max Memory :      4728 MB
    Max Swap   :      5463 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z048-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z048-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z048-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z048-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1540>
Subject: Job 4389172: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1540>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000078> was used as the working directory.
Started at Wed Oct 24 15:04:35 2012
Results reported at Wed Oct 24 15:05:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000078.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000078.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z049-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z049-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z049-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000078.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.59 sec.
    Max Memory :      4728 MB
    Max Swap   :      5466 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z049-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z049-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z049-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z049-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4389181: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000079> was used as the working directory.
Started at Wed Oct 24 15:04:35 2012
Results reported at Wed Oct 24 15:04:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000079.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000079.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z050-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z050-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z050-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000079.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.01 sec.
    Max Memory :         7 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z050-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z050-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z050-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z050-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1549>
Subject: Job 4389195: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1549>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000080> was used as the working directory.
Started at Wed Oct 24 15:04:35 2012
Results reported at Wed Oct 24 15:05:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000080.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000080.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z051-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z051-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z051-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000080.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.42 sec.
    Max Memory :        13 MB
    Max Swap   :        50 MB

    Max Processes  :         4
    Max Threads    :         4

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z051-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z051-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z051-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z051-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1543>
Subject: Job 4389204: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1543>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000081> was used as the working directory.
Started at Wed Oct 24 15:04:47 2012
Results reported at Wed Oct 24 15:05:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000081.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000081.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z052-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z052-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z052-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000081.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.79 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z052-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z052-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z052-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z052-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1528>
Subject: Job 4389217: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1528>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000082> was used as the working directory.
Started at Wed Oct 24 15:04:51 2012
Results reported at Wed Oct 24 15:05:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000082.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000082.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z053-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z053-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z053-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000082.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.95 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z053-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z053-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z053-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z053-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 4389231: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000083> was used as the working directory.
Started at Wed Oct 24 15:05:05 2012
Results reported at Wed Oct 24 15:05:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000083.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000083.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z054-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z054-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z054-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000083.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.94 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z054-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z054-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z054-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z054-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4389243: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000084> was used as the working directory.
Started at Wed Oct 24 15:05:17 2012
Results reported at Wed Oct 24 15:05:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000084.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000084.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z055-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z055-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z055-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000084.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.78 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z055-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z055-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z055-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z055-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4389258: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000085> was used as the working directory.
Started at Wed Oct 24 15:05:17 2012
Results reported at Wed Oct 24 15:05:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000085.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000085.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z056-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z056-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z056-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000085.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.16 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z056-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z056-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z056-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z056-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4389271: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000086> was used as the working directory.
Started at Wed Oct 24 15:05:17 2012
Results reported at Wed Oct 24 15:05:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000086.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000086.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z057-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z057-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z057-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000086.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.83 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z057-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z057-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z057-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z057-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1645>
Subject: Job 4389284: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000087> was used as the working directory.
Started at Wed Oct 24 15:05:17 2012
Results reported at Wed Oct 24 15:05:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000087.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000087.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z058-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z058-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z058-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000087.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.66 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z058-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z058-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z058-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z058-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1416>
Subject: Job 4389300: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1416>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000088> was used as the working directory.
Started at Wed Oct 24 15:05:17 2012
Results reported at Wed Oct 24 15:05:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000088.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000088.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z059-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z059-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z059-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000088.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     36.15 sec.
    Max Memory :      4723 MB
    Max Swap   :      5463 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z059-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z059-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z059-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z059-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4389314: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000089> was used as the working directory.
Started at Wed Oct 24 15:05:26 2012
Results reported at Wed Oct 24 15:05:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000089.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000089.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z060-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z060-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z060-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000089.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.58 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z060-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z060-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z060-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z060-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1653>
Subject: Job 4389326: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1653>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000090> was used as the working directory.
Started at Wed Oct 24 15:05:26 2012
Results reported at Wed Oct 24 15:05:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000090.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000090.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z061-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z061-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z061-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000090.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.27 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z061-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z061-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z061-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z061-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1644>
Subject: Job 4389335: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000091> was used as the working directory.
Started at Wed Oct 24 15:05:26 2012
Results reported at Wed Oct 24 15:05:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000091.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000091.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-17-Z062-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-17-Z062-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z062-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000091.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.55 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-17-Z062-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-17-Z062-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-17-Z062-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-17-Z062-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 4389347: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000092> was used as the working directory.
Started at Wed Oct 24 15:05:26 2012
Results reported at Wed Oct 24 15:05:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000092.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000092.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-35-3615-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-35-3615-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-35-3615-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000092.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.03 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-35-3615-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-35-3615-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-35-3615-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-35-3615-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4389355: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000093> was used as the working directory.
Started at Wed Oct 24 15:05:26 2012
Results reported at Wed Oct 24 15:05:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000093.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000093.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-35-4122-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-35-4122-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-35-4122-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000093.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.81 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-35-4122-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-35-4122-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-35-4122-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-35-4122-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1726>
Subject: Job 4389367: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000094> was used as the working directory.
Started at Wed Oct 24 15:05:26 2012
Results reported at Wed Oct 24 15:05:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000094.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000094.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-35-4123-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-35-4123-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-35-4123-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000094.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.46 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-35-4123-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-35-4123-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-35-4123-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-35-4123-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4389375: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000095> was used as the working directory.
Started at Wed Oct 24 15:05:26 2012
Results reported at Wed Oct 24 15:05:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000095.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000095.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-35-5375-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-35-5375-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-35-5375-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000095.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.71 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-35-5375-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-35-5375-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-35-5375-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-35-5375-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1540>
Subject: Job 4389386: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1540>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000096> was used as the working directory.
Started at Wed Oct 24 15:05:37 2012
Results reported at Wed Oct 24 15:06:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000096.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000096.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-4625-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-4625-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4625-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000096.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.56 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4625-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-4625-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-4625-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-4625-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1546>
Subject: Job 4389397: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000097> was used as the working directory.
Started at Wed Oct 24 15:05:37 2012
Results reported at Wed Oct 24 15:06:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000097.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000097.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-4626-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-4626-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4626-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000097.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.36 sec.
    Max Memory :      4721 MB
    Max Swap   :      5462 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4626-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-4626-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-4626-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-4626-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4389405: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000098> was used as the working directory.
Started at Wed Oct 24 15:05:37 2012
Results reported at Wed Oct 24 15:06:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000098.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000098.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-4627-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-4627-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4627-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000098.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.93 sec.
    Max Memory :      4495 MB
    Max Swap   :      5404 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4627-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-4627-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-4627-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-4627-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 4389415: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000099> was used as the working directory.
Started at Wed Oct 24 15:05:49 2012
Results reported at Wed Oct 24 15:06:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000099.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000099.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-4628-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-4628-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4628-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000099.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.41 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4628-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-4628-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-4628-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-4628-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1536>
Subject: Job 4389425: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1536>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000100> was used as the working directory.
Started at Wed Oct 24 15:05:57 2012
Results reported at Wed Oct 24 15:06:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000100.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000100.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-4629-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-4629-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4629-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000100.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.79 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4629-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-4629-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-4629-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-4629-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4389435: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000101> was used as the working directory.
Started at Wed Oct 24 15:06:18 2012
Results reported at Wed Oct 24 15:06:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000101.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000101.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-4630-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-4630-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4630-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000101.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.17 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4630-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-4630-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-4630-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-4630-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4389449: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000102> was used as the working directory.
Started at Wed Oct 24 15:06:18 2012
Results reported at Wed Oct 24 15:06:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000102.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000102.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-4631-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-4631-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4631-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000102.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.95 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4631-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-4631-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-4631-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-4631-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 4389459: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000103> was used as the working directory.
Started at Wed Oct 24 15:06:18 2012
Results reported at Wed Oct 24 15:06:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000103.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000103.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-4632-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-4632-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4632-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000103.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.28 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-4632-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-4632-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-4632-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-4632-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4389549: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000104> was used as the working directory.
Started at Wed Oct 24 15:06:25 2012
Results reported at Wed Oct 24 15:06:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000104.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000104.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-38-6178-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-38-6178-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-6178-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000104.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.27 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-38-6178-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-38-6178-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-38-6178-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-38-6178-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1726>
Subject: Job 4389558: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000105> was used as the working directory.
Started at Wed Oct 24 15:06:25 2012
Results reported at Wed Oct 24 15:06:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000105.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000105.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2655-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2655-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2655-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000105.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.78 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2655-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2655-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2655-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2655-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4389567: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000106> was used as the working directory.
Started at Wed Oct 24 15:06:25 2012
Results reported at Wed Oct 24 15:06:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000106.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000106.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2656-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2656-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2656-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000106.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.88 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2656-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2656-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2656-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2656-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1538>
Subject: Job 4389580: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1538>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000107> was used as the working directory.
Started at Wed Oct 24 15:06:32 2012
Results reported at Wed Oct 24 15:07:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000107.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000107.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2657-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2657-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2657-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000107.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.35 sec.
    Max Memory :        13 MB
    Max Swap   :        50 MB

    Max Processes  :         4
    Max Threads    :         4

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2657-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2657-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2657-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2657-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4389587: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000108> was used as the working directory.
Started at Wed Oct 24 15:06:37 2012
Results reported at Wed Oct 24 15:06:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000108.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000108.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2659-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2659-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2659-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000108.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.99 sec.
    Max Memory :         7 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2659-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2659-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2659-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2659-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 4389604: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000109> was used as the working directory.
Started at Wed Oct 24 15:06:49 2012
Results reported at Wed Oct 24 15:07:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000109.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000109.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2661-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2661-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2661-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000109.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.28 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2661-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2661-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2661-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2661-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4389620: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000110> was used as the working directory.
Started at Wed Oct 24 15:06:49 2012
Results reported at Wed Oct 24 15:07:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000110.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000110.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2662-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2662-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2662-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000110.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.74 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2662-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2662-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2662-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2662-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1553>
Subject: Job 4389635: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1553>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000111> was used as the working directory.
Started at Wed Oct 24 15:07:18 2012
Results reported at Wed Oct 24 15:09:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000111.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000111.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2665-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2665-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2665-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000111.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     51.90 sec.
    Max Memory :      4701 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2665-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2665-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2665-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2665-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1431>
Subject: Job 4389652: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1431>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000112> was used as the working directory.
Started at Wed Oct 24 15:07:18 2012
Results reported at Wed Oct 24 15:07:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000112.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000112.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2666-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2666-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2666-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000112.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.72 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2666-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2666-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2666-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2666-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4389662: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000113> was used as the working directory.
Started at Wed Oct 24 15:07:18 2012
Results reported at Wed Oct 24 15:07:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000113.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000113.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-2668-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-2668-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2668-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000113.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.74 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-2668-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-2668-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-2668-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-2668-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4389678: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000114> was used as the working directory.
Started at Wed Oct 24 15:07:18 2012
Results reported at Wed Oct 24 15:07:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000114.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000114.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-3396-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-3396-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-3396-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000114.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.88 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-3396-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-3396-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-3396-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-3396-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 4389686: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000115> was used as the working directory.
Started at Wed Oct 24 15:07:18 2012
Results reported at Wed Oct 24 15:07:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000115.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000115.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-3398-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-3398-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-3398-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000115.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.61 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-3398-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-3398-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-3398-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-3398-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4389697: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000116> was used as the working directory.
Started at Wed Oct 24 15:07:27 2012
Results reported at Wed Oct 24 15:07:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000116.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000116.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-3918-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-3918-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-3918-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000116.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.02 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-3918-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-3918-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-3918-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-3918-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1653>
Subject: Job 4389704: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1653>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000117> was used as the working directory.
Started at Wed Oct 24 15:07:27 2012
Results reported at Wed Oct 24 15:07:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000117.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000117.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-3919-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-3919-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-3919-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000117.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.82 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-3919-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-3919-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-3919-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-3919-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1726>
Subject: Job 4389716: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000118> was used as the working directory.
Started at Wed Oct 24 15:07:27 2012
Results reported at Wed Oct 24 15:07:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000118.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000118.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-4112-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-4112-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-4112-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000118.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.04 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-4112-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-4112-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-4112-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-4112-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 4389725: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000119> was used as the working directory.
Started at Wed Oct 24 15:07:27 2012
Results reported at Wed Oct 24 15:07:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000119.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000119.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-5643-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-5643-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-5643-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000119.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.99 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-5643-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-5643-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-5643-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-5643-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1729>
Subject: Job 4389735: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1729>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000120> was used as the working directory.
Started at Wed Oct 24 15:07:27 2012
Results reported at Wed Oct 24 15:07:55 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000120.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000120.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-5645-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-5645-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-5645-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000120.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.30 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-5645-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-5645-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-5645-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-5645-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1546>
Subject: Job 4389744: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000121> was used as the working directory.
Started at Wed Oct 24 15:07:39 2012
Results reported at Wed Oct 24 15:08:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000121.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000121.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6144-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6144-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6144-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000121.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.82 sec.
    Max Memory :        13 MB
    Max Swap   :        50 MB

    Max Processes  :         4
    Max Threads    :         4

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6144-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6144-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6144-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6144-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1540>
Subject: Job 4389754: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1540>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000122> was used as the working directory.
Started at Wed Oct 24 15:07:39 2012
Results reported at Wed Oct 24 15:08:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000122.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000122.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6145-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6145-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6145-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000122.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.28 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6145-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6145-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6145-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6145-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4389765: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000123> was used as the working directory.
Started at Wed Oct 24 15:07:39 2012
Results reported at Wed Oct 24 15:08:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000123.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000123.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6146-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6146-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6146-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000123.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.04 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6146-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6146-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6146-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6146-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4389774: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000124> was used as the working directory.
Started at Wed Oct 24 15:07:49 2012
Results reported at Wed Oct 24 15:08:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000124.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000124.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6147-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6147-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6147-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000124.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.94 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6147-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6147-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6147-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6147-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4389782: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000125> was used as the working directory.
Started at Wed Oct 24 15:08:19 2012
Results reported at Wed Oct 24 15:08:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000125.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000125.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6148-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6148-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6148-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000125.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.85 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6148-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6148-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6148-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6148-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4389791: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000126> was used as the working directory.
Started at Wed Oct 24 15:08:19 2012
Results reported at Wed Oct 24 15:08:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000126.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000126.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6774-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6774-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6774-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000126.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.86 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6774-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6774-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6774-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6774-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4389796: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000127> was used as the working directory.
Started at Wed Oct 24 15:08:19 2012
Results reported at Wed Oct 24 15:08:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000127.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000127.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6775-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6775-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6775-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000127.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.00 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6775-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6775-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6775-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6775-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1730>
Subject: Job 4389804: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1730>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000128> was used as the working directory.
Started at Wed Oct 24 15:08:19 2012
Results reported at Wed Oct 24 15:08:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000128.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000128.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6776-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6776-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6776-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000128.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.10 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6776-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6776-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6776-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6776-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 4389810: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000129> was used as the working directory.
Started at Wed Oct 24 15:08:19 2012
Results reported at Wed Oct 24 15:08:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000129.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000129.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6777-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6777-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6777-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000129.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.15 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6777-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6777-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6777-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6777-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4389818: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000130> was used as the working directory.
Started at Wed Oct 24 15:08:19 2012
Results reported at Wed Oct 24 15:08:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000130.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000130.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6778-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6778-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6778-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000130.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.19 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6778-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6778-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6778-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6778-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4389826: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000131> was used as the working directory.
Started at Wed Oct 24 15:08:28 2012
Results reported at Wed Oct 24 15:08:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000131.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000131.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-44-6779-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-44-6779-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6779-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000131.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.68 sec.
    Max Memory :         5 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-44-6779-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-44-6779-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-44-6779-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-44-6779-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1644>
Subject: Job 4389834: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000132> was used as the working directory.
Started at Wed Oct 24 15:08:28 2012
Results reported at Wed Oct 24 15:08:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000132.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000132.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4486-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4486-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4486-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000132.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.47 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4486-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4486-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4486-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4486-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1535>
Subject: Job 4389839: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1535>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000133> was used as the working directory.
Started at Wed Oct 24 15:08:28 2012
Results reported at Wed Oct 24 15:09:02 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000133.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000133.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4487-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4487-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4487-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000133.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     37.00 sec.
    Max Memory :      4662 MB
    Max Swap   :      5468 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4487-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4487-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4487-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4487-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4389847: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000134> was used as the working directory.
Started at Wed Oct 24 15:08:28 2012
Results reported at Wed Oct 24 15:08:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000134.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000134.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4488-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4488-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4488-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000134.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.15 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4488-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4488-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4488-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4488-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 4389855: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000135> was used as the working directory.
Started at Wed Oct 24 15:08:28 2012
Results reported at Wed Oct 24 15:08:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000135.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000135.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4490-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4490-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4490-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000135.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.30 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4490-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4490-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4490-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4490-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4389860: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000136> was used as the working directory.
Started at Wed Oct 24 15:08:28 2012
Results reported at Wed Oct 24 15:08:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000136.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000136.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4494-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4494-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4494-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000136.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.88 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4494-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4494-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4494-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4494-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1701>
Subject: Job 4389872: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1701>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000137> was used as the working directory.
Started at Wed Oct 24 15:08:37 2012
Results reported at Wed Oct 24 15:21:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000137.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000137.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4501-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4501-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4501-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000137.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.29 sec.
    Max Memory :      4738 MB
    Max Swap   :      5464 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4501-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4501-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4501-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4501-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1546>
Subject: Job 4389881: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000138> was used as the working directory.
Started at Wed Oct 24 15:08:39 2012
Results reported at Wed Oct 24 15:09:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000138.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000138.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4505-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4505-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4505-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000138.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.80 sec.
    Max Memory :        13 MB
    Max Swap   :        58 MB

    Max Processes  :         4
    Max Threads    :         5

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4505-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4505-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4505-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4505-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 4389891: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000139> was used as the working directory.
Started at Wed Oct 24 15:08:39 2012
Results reported at Wed Oct 24 15:09:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000139.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000139.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4506-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4506-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4506-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000139.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.36 sec.
    Max Memory :      4727 MB
    Max Swap   :      5468 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4506-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4506-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4506-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4506-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1529>
Subject: Job 4389903: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1529>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000140> was used as the working directory.
Started at Wed Oct 24 15:08:49 2012
Results reported at Wed Oct 24 15:22:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000140.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000140.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4507-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4507-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4507-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000140.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     87.25 sec.
    Max Memory :      4720 MB
    Max Swap   :      5527 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4507-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4507-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4507-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4507-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 4389914: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000141> was used as the working directory.
Started at Wed Oct 24 15:08:49 2012
Results reported at Wed Oct 24 15:09:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000141.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000141.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4510-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4510-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4510-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000141.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.66 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4510-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4510-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4510-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4510-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1536>
Subject: Job 4389928: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1536>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000142> was used as the working directory.
Started at Wed Oct 24 15:08:57 2012
Results reported at Wed Oct 24 15:09:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000142.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000142.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4512-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4512-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4512-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000142.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.51 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4512-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4512-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4512-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4512-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1702>
Subject: Job 4389938: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000143> was used as the working directory.
Started at Wed Oct 24 15:09:21 2012
Results reported at Wed Oct 24 15:09:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000143.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000143.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-4514-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-4514-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4514-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000143.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.36 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-4514-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-4514-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-4514-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-4514-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4389952: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000144> was used as the working directory.
Started at Wed Oct 24 15:09:21 2012
Results reported at Wed Oct 24 15:09:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000144.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000144.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-6742-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-6742-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6742-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000144.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.39 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6742-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-6742-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-6742-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-6742-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1730>
Subject: Job 4389960: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1730>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000145> was used as the working directory.
Started at Wed Oct 24 15:09:21 2012
Results reported at Wed Oct 24 15:09:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000145.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000145.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-6743-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-6743-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6743-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000145.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.60 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6743-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-6743-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-6743-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-6743-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 4389969: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000146> was used as the working directory.
Started at Wed Oct 24 15:09:21 2012
Results reported at Wed Oct 24 15:09:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000146.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000146.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-6744-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-6744-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6744-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000146.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.04 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6744-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-6744-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-6744-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-6744-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1644>
Subject: Job 4389984: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000147> was used as the working directory.
Started at Wed Oct 24 15:09:28 2012
Results reported at Wed Oct 24 15:09:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000147.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000147.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-6745-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-6745-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6745-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000147.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.51 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6745-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-6745-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-6745-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-6745-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1421>
Subject: Job 4389992: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1421>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000148> was used as the working directory.
Started at Wed Oct 24 15:09:28 2012
Results reported at Wed Oct 24 15:10:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000148.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000148.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-49-6767-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-49-6767-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6767-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000148.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.95 sec.
    Max Memory :        10 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-49-6767-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-49-6767-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-49-6767-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-49-6767-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1653>
Subject: Job 4390000: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1653>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000149> was used as the working directory.
Started at Wed Oct 24 15:09:28 2012
Results reported at Wed Oct 24 15:09:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000149.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000149.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5044-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5044-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5044-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000149.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.29 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5044-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5044-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5044-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5044-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1535>
Subject: Job 4390010: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1535>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000150> was used as the working directory.
Started at Wed Oct 24 15:09:28 2012
Results reported at Wed Oct 24 15:09:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000150.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000150.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5045-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5045-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5045-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000150.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.89 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5045-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5045-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5045-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5045-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1726>
Subject: Job 4390023: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000151> was used as the working directory.
Started at Wed Oct 24 15:09:28 2012
Results reported at Wed Oct 24 15:09:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000151.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000151.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5049-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5049-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5049-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000151.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.05 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5049-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5049-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5049-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5049-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4390034: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000152> was used as the working directory.
Started at Wed Oct 24 15:09:28 2012
Results reported at Wed Oct 24 15:09:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000152.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000152.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5051-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5051-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5051-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000152.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.61 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5051-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5051-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5051-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5051-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4390046: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000153> was used as the working directory.
Started at Wed Oct 24 15:09:28 2012
Results reported at Wed Oct 24 15:09:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000153.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000153.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5055-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5055-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5055-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000153.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.57 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5055-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5055-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5055-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5055-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1546>
Subject: Job 4390060: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000154> was used as the working directory.
Started at Wed Oct 24 15:09:40 2012
Results reported at Wed Oct 24 15:10:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000154.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000154.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5066-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5066-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5066-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000154.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.34 sec.
    Max Memory :      4723 MB
    Max Swap   :      5470 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5066-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5066-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5066-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5066-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 4390071: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000155> was used as the working directory.
Started at Wed Oct 24 15:09:40 2012
Results reported at Wed Oct 24 15:10:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000155.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000155.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5068-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5068-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5068-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000155.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.64 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5068-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5068-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5068-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5068-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 4390082: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000156> was used as the working directory.
Started at Wed Oct 24 15:09:49 2012
Results reported at Wed Oct 24 15:10:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000156.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000156.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5072-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5072-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5072-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000156.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.02 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5072-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5072-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5072-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5072-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1533>
Subject: Job 4390093: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1533>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000157> was used as the working directory.
Started at Wed Oct 24 15:09:49 2012
Results reported at Wed Oct 24 15:10:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000157.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000157.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5930-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5930-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5930-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000157.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.34 sec.
    Max Memory :      4718 MB
    Max Swap   :      5455 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5930-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5930-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5930-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5930-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1536>
Subject: Job 4390104: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1536>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000158> was used as the working directory.
Started at Wed Oct 24 15:09:58 2012
Results reported at Wed Oct 24 15:10:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000158.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000158.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5931-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5931-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5931-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000158.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.92 sec.
    Max Memory :      4717 MB
    Max Swap   :      5522 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5931-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5931-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5931-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5931-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1541>
Subject: Job 4390116: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1541>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000159> was used as the working directory.
Started at Wed Oct 24 15:10:02 2012
Results reported at Wed Oct 24 15:10:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000159.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000159.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5932-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5932-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5932-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000159.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.40 sec.
    Max Memory :      4715 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5932-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5932-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5932-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5932-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1553>
Subject: Job 4390126: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1553>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000160> was used as the working directory.
Started at Wed Oct 24 15:10:21 2012
Results reported at Wed Oct 24 15:10:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000160.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000160.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5933-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5933-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5933-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000160.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.40 sec.
    Max Memory :        10 MB
    Max Swap   :        38 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5933-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5933-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5933-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5933-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4390134: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000161> was used as the working directory.
Started at Wed Oct 24 15:10:21 2012
Results reported at Wed Oct 24 15:10:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000161.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000161.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5935-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5935-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5935-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000161.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.89 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5935-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5935-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5935-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5935-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1645>
Subject: Job 4390143: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000162> was used as the working directory.
Started at Wed Oct 24 15:10:21 2012
Results reported at Wed Oct 24 15:10:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000162.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000162.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5936-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5936-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5936-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000162.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.04 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5936-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5936-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5936-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5936-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 4390156: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000163> was used as the working directory.
Started at Wed Oct 24 15:10:21 2012
Results reported at Wed Oct 24 15:10:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000163.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000163.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5939-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5939-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5939-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000163.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.32 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5939-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5939-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5939-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5939-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1416>
Subject: Job 4390162: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1416>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000164> was used as the working directory.
Started at Wed Oct 24 15:10:21 2012
Results reported at Wed Oct 24 15:11:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000164.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000164.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5941-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5941-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5941-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000164.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     33.85 sec.
    Max Memory :      4703 MB
    Max Swap   :      5455 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5941-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5941-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5941-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5941-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1535>
Subject: Job 4390173: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1535>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000165> was used as the working directory.
Started at Wed Oct 24 15:10:29 2012
Results reported at Wed Oct 24 15:10:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000165.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000165.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5942-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5942-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5942-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000165.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.89 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5942-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5942-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5942-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5942-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4390183: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000166> was used as the working directory.
Started at Wed Oct 24 15:10:29 2012
Results reported at Wed Oct 24 15:10:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000166.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000166.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5944-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5944-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5944-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000166.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.02 sec.
    Max Memory :         5 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5944-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5944-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5944-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5944-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 4390197: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000167> was used as the working directory.
Started at Wed Oct 24 15:10:29 2012
Results reported at Wed Oct 24 15:10:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000167.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000167.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-5946-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-5946-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5946-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000167.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.44 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-5946-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-5946-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-5946-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-5946-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 4390206: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000168> was used as the working directory.
Started at Wed Oct 24 15:10:29 2012
Results reported at Wed Oct 24 15:10:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000168.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000168.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-6590-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-6590-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6590-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000168.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.94 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6590-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-6590-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-6590-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-6590-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4390215: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000169> was used as the working directory.
Started at Wed Oct 24 15:10:29 2012
Results reported at Wed Oct 24 15:10:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000169.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000169.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-6591-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-6591-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6591-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000169.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.63 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6591-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-6591-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-6591-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-6591-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4390226: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000170> was used as the working directory.
Started at Wed Oct 24 15:10:29 2012
Results reported at Wed Oct 24 15:11:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000170.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000170.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-6592-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-6592-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6592-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000170.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.19 sec.
    Max Memory :      4499 MB
    Max Swap   :      5467 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6592-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-6592-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-6592-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-6592-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 4390233: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000171> was used as the working directory.
Started at Wed Oct 24 15:10:32 2012
Results reported at Wed Oct 24 15:10:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000171.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000171.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-6593-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-6593-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6593-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000171.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.22 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6593-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-6593-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-6593-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-6593-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1546>
Subject: Job 4390240: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000172> was used as the working directory.
Started at Wed Oct 24 15:10:41 2012
Results reported at Wed Oct 24 15:11:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000172.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000172.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-6594-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-6594-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6594-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000172.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.24 sec.
    Max Memory :      4718 MB
    Max Swap   :      5464 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6594-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-6594-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-6594-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-6594-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1540>
Subject: Job 4390246: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1540>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000173> was used as the working directory.
Started at Wed Oct 24 15:10:41 2012
Results reported at Wed Oct 24 15:11:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000173.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000173.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-6595-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-6595-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6595-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000173.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.42 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6595-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-6595-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-6595-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-6595-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1555>
Subject: Job 4390253: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1555>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000174> was used as the working directory.
Started at Wed Oct 24 15:10:43 2012
Results reported at Wed Oct 24 15:11:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000174.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000174.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-50-6597-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-50-6597-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6597-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000174.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.67 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-50-6597-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-50-6597-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-50-6597-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-50-6597-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 4390258: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000175> was used as the working directory.
Started at Wed Oct 24 15:10:49 2012
Results reported at Wed Oct 24 15:11:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000175.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000175.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-55-1592-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-55-1592-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-1592-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000175.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.61 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-1592-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-55-1592-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-55-1592-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-55-1592-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1707>
Subject: Job 4390266: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1707>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000176> was used as the working directory.
Started at Wed Oct 24 15:10:49 2012
Results reported at Wed Oct 24 15:11:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000176.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000176.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-55-1594-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-55-1594-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-1594-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000176.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.79 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-1594-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-55-1594-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-55-1594-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-55-1594-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1533>
Subject: Job 4390272: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1533>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000177> was used as the working directory.
Started at Wed Oct 24 15:10:49 2012
Results reported at Wed Oct 24 15:11:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000177.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000177.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-55-1595-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-55-1595-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-1595-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000177.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.14 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-1595-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-55-1595-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-55-1595-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-55-1595-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1536>
Subject: Job 4390278: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1536>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000178> was used as the working directory.
Started at Wed Oct 24 15:10:57 2012
Results reported at Wed Oct 24 15:11:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000178.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000178.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-55-1596-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-55-1596-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-1596-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000178.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.63 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-1596-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-55-1596-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-55-1596-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-55-1596-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1528>
Subject: Job 4390283: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1528>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000179> was used as the working directory.
Started at Wed Oct 24 15:11:03 2012
Results reported at Wed Oct 24 15:11:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000179.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000179.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-55-5899-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-55-5899-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-5899-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000179.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     34.13 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-5899-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-55-5899-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-55-5899-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-55-5899-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1702>
Subject: Job 4390290: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000180> was used as the working directory.
Started at Wed Oct 24 15:11:20 2012
Results reported at Wed Oct 24 15:11:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000180.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000180.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-55-6543-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-55-6543-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-6543-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000180.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.01 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-6543-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-55-6543-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-55-6543-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-55-6543-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4390296: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000181> was used as the working directory.
Started at Wed Oct 24 15:11:20 2012
Results reported at Wed Oct 24 15:11:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000181.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000181.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-55-6642-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-55-6642-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-6642-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000181.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.15 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-6642-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-55-6642-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-55-6642-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-55-6642-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 4390302: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000182> was used as the working directory.
Started at Wed Oct 24 15:11:20 2012
Results reported at Wed Oct 24 15:11:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000182.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000182.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-55-6712-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-55-6712-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-6712-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000182.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.84 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-55-6712-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-55-6712-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-55-6712-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-55-6712-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1730>
Subject: Job 4390310: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1730>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000183> was used as the working directory.
Started at Wed Oct 24 15:11:20 2012
Results reported at Wed Oct 24 15:11:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000183.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000183.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-1676-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-1676-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-1676-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000183.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.02 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-1676-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-1676-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-1676-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-1676-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1416>
Subject: Job 4390316: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1416>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000184> was used as the working directory.
Started at Wed Oct 24 15:11:20 2012
Results reported at Wed Oct 24 15:12:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000184.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000184.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-1677-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-1677-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-1677-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000184.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.74 sec.
    Max Memory :      4711 MB
    Max Swap   :      5517 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-1677-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-1677-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-1677-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-1677-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4390327: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000185> was used as the working directory.
Started at Wed Oct 24 15:11:30 2012
Results reported at Wed Oct 24 15:11:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000185.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000185.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-1678-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-1678-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-1678-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000185.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.18 sec.
    Max Memory :         5 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-1678-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-1678-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-1678-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-1678-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1653>
Subject: Job 4390332: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1653>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000186> was used as the working directory.
Started at Wed Oct 24 15:11:30 2012
Results reported at Wed Oct 24 15:11:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000186.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000186.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-1680-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-1680-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-1680-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000186.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.49 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-1680-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-1680-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-1680-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-1680-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1421>
Subject: Job 4390338: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1421>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000187> was used as the working directory.
Started at Wed Oct 24 15:11:30 2012
Results reported at Wed Oct 24 15:12:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000187.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000187.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-5774-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-5774-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5774-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000187.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.30 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5774-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-5774-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-5774-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-5774-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1535>
Subject: Job 4390346: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1535>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000188> was used as the working directory.
Started at Wed Oct 24 15:11:30 2012
Results reported at Wed Oct 24 15:12:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000188.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000188.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-5775-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-5775-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5775-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000188.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.15 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5775-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-5775-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-5775-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-5775-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 4390351: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000189> was used as the working directory.
Started at Wed Oct 24 15:11:30 2012
Results reported at Wed Oct 24 15:11:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000189.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000189.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-5778-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-5778-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5778-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000189.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.91 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5778-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-5778-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-5778-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-5778-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4390361: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000190> was used as the working directory.
Started at Wed Oct 24 15:11:30 2012
Results reported at Wed Oct 24 15:11:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000190.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000190.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-5779-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-5779-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5779-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000190.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     22.10 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5779-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-5779-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-5779-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-5779-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4390368: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000191> was used as the working directory.
Started at Wed Oct 24 15:11:30 2012
Results reported at Wed Oct 24 15:11:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000191.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000191.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-5781-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-5781-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5781-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000191.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.09 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5781-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-5781-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-5781-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-5781-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4390383: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000192> was used as the working directory.
Started at Wed Oct 24 15:11:40 2012
Results reported at Wed Oct 24 15:11:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000192.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000192.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-64-5815-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-64-5815-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5815-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000192.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.28 sec.
    Max Memory :         7 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-64-5815-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-64-5815-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-64-5815-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-64-5815-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1549>
Subject: Job 4390389: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1549>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000193> was used as the working directory.
Started at Wed Oct 24 15:11:40 2012
Results reported at Wed Oct 24 15:12:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000193.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000193.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-3770-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-3770-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3770-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000193.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.62 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3770-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-3770-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-3770-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-3770-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 4390397: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000194> was used as the working directory.
Started at Wed Oct 24 15:11:50 2012
Results reported at Wed Oct 24 15:12:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000194.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000194.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-3771-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-3771-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3771-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000194.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.28 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3771-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-3771-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-3771-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-3771-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1542>
Subject: Job 4390404: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1542>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000195> was used as the working directory.
Started at Wed Oct 24 15:11:50 2012
Results reported at Wed Oct 24 15:12:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000195.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000195.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-3772-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-3772-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3772-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000195.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.90 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3772-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-3772-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-3772-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-3772-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1707>
Subject: Job 4390411: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1707>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000196> was used as the working directory.
Started at Wed Oct 24 15:11:50 2012
Results reported at Wed Oct 24 15:12:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000196.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000196.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-3773-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-3773-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3773-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000196.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.93 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3773-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-3773-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-3773-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-3773-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1644>
Subject: Job 4390420: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000197> was used as the working directory.
Started at Wed Oct 24 15:11:58 2012
Results reported at Wed Oct 24 15:12:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000197.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000197.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-3774-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-3774-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3774-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000197.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.66 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-3774-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-3774-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-3774-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-3774-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1536>
Subject: Job 4390426: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1536>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000198> was used as the working directory.
Started at Wed Oct 24 15:11:58 2012
Results reported at Wed Oct 24 15:12:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000198.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000198.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-4679-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-4679-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-4679-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000198.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.42 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-4679-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-4679-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-4679-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-4679-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1534>
Subject: Job 4390435: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1534>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000199> was used as the working directory.
Started at Wed Oct 24 15:12:02 2012
Results reported at Wed Oct 24 15:12:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000199.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000199.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-6215-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-6215-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-6215-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000199.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.67 sec.
    Max Memory :        13 MB
    Max Swap   :        50 MB

    Max Processes  :         4
    Max Threads    :         5

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-6215-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-6215-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-6215-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-6215-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4390442: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000200> was used as the working directory.
Started at Wed Oct 24 15:12:20 2012
Results reported at Wed Oct 24 15:12:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000200.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000200.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-6216-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-6216-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-6216-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000200.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.48 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-6216-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-6216-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-6216-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-6216-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4390449: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000201> was used as the working directory.
Started at Wed Oct 24 15:12:20 2012
Results reported at Wed Oct 24 15:12:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000201.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000201.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-67-6217-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-67-6217-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-6217-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000201.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.82 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-67-6217-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-67-6217-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-67-6217-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-67-6217-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4390457: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000202> was used as the working directory.
Started at Wed Oct 24 15:12:20 2012
Results reported at Wed Oct 24 15:12:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000202.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000202.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-71-6725-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-71-6725-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-71-6725-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000202.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.83 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-71-6725-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-71-6725-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-71-6725-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-71-6725-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4390463: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000203> was used as the working directory.
Started at Wed Oct 24 15:12:20 2012
Results reported at Wed Oct 24 15:12:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000203.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000203.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4658-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4658-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4658-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000203.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.75 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4658-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4658-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4658-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4658-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4390472: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000204> was used as the working directory.
Started at Wed Oct 24 15:12:31 2012
Results reported at Wed Oct 24 15:12:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000204.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000204.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4659-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4659-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4659-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000204.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.42 sec.
    Max Memory :         5 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4659-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4659-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4659-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4659-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4390478: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000205> was used as the working directory.
Started at Wed Oct 24 15:12:31 2012
Results reported at Wed Oct 24 15:12:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000205.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000205.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4662-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4662-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4662-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000205.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.08 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4662-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4662-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4662-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4662-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4390487: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000206> was used as the working directory.
Started at Wed Oct 24 15:12:31 2012
Results reported at Wed Oct 24 15:12:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000206.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000206.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4666-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4666-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4666-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000206.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.02 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4666-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4666-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4666-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4666-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 4390496: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000207> was used as the working directory.
Started at Wed Oct 24 15:12:31 2012
Results reported at Wed Oct 24 15:12:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000207.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000207.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4668-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4668-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4668-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000207.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.46 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4668-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4668-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4668-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4668-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4390501: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000208> was used as the working directory.
Started at Wed Oct 24 15:12:31 2012
Results reported at Wed Oct 24 15:12:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000208.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000208.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4670-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4670-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4670-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000208.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.56 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4670-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4670-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4670-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4670-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4390510: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000209> was used as the working directory.
Started at Wed Oct 24 15:12:31 2012
Results reported at Wed Oct 24 15:12:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000209.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000209.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4675-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4675-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4675-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000209.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.42 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4675-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4675-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4675-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4675-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4390517: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000210> was used as the working directory.
Started at Wed Oct 24 15:12:41 2012
Results reported at Wed Oct 24 15:13:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000210.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000210.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4676-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4676-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4676-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000210.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.58 sec.
    Max Memory :         7 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4676-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4676-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4676-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4676-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4390524: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000211> was used as the working directory.
Started at Wed Oct 24 15:12:41 2012
Results reported at Wed Oct 24 15:13:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000211.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000211.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-73-4677-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-73-4677-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4677-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000211.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.93 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-73-4677-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-73-4677-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-73-4677-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-73-4677-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4390530: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000212> was used as the working directory.
Started at Wed Oct 24 15:12:50 2012
Results reported at Wed Oct 24 15:13:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000212.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000212.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-5122-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-5122-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5122-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000212.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.95 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5122-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-5122-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-5122-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-5122-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1707>
Subject: Job 4390540: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1707>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000213> was used as the working directory.
Started at Wed Oct 24 15:12:50 2012
Results reported at Wed Oct 24 15:13:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000213.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000213.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-5125-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-5125-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5125-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000213.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.53 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5125-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-5125-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-5125-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-5125-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 4390547: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000214> was used as the working directory.
Started at Wed Oct 24 15:12:50 2012
Results reported at Wed Oct 24 15:13:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000214.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000214.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-5126-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-5126-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5126-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000214.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.36 sec.
    Max Memory :        13 MB
    Max Swap   :        50 MB

    Max Processes  :         4
    Max Threads    :         4

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5126-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-5126-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-5126-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-5126-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1427>
Subject: Job 4390555: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1427>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000215> was used as the working directory.
Started at Wed Oct 24 15:12:58 2012
Results reported at Wed Oct 24 15:13:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000215.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000215.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-5146-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-5146-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5146-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000215.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.25 sec.
    Max Memory :        10 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5146-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-5146-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-5146-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-5146-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1541>
Subject: Job 4390562: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1541>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000216> was used as the working directory.
Started at Wed Oct 24 15:13:01 2012
Results reported at Wed Oct 24 15:13:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000216.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000216.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-5147-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-5147-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5147-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000216.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     32.34 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-5147-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-5147-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-5147-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-5147-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1554>
Subject: Job 4390568: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000217> was used as the working directory.
Started at Wed Oct 24 15:13:07 2012
Results reported at Wed Oct 24 15:17:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000217.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000217.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-6203-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-6203-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6203-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000217.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     64.01 sec.
    Max Memory :      4723 MB
    Max Swap   :      5463 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6203-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-6203-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-6203-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-6203-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4390573: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000218> was used as the working directory.
Started at Wed Oct 24 15:13:22 2012
Results reported at Wed Oct 24 15:13:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000218.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000218.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-6205-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-6205-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6205-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000218.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.50 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6205-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-6205-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-6205-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-6205-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1702>
Subject: Job 4390585: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000219> was used as the working directory.
Started at Wed Oct 24 15:13:22 2012
Results reported at Wed Oct 24 15:13:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000219.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000219.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-6206-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-6206-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6206-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000219.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.82 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6206-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-6206-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-6206-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-6206-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1730>
Subject: Job 4390590: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1730>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000220> was used as the working directory.
Started at Wed Oct 24 15:13:22 2012
Results reported at Wed Oct 24 15:13:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000220.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000220.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-6207-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-6207-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6207-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000220.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.28 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6207-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-6207-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-6207-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-6207-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1421>
Subject: Job 4390603: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1421>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000221> was used as the working directory.
Started at Wed Oct 24 15:13:32 2012
Results reported at Wed Oct 24 15:14:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000221.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000221.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-6211-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-6211-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6211-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000221.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.99 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6211-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-6211-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-6211-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-6211-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1726>
Subject: Job 4390612: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000222> was used as the working directory.
Started at Wed Oct 24 15:13:32 2012
Results reported at Wed Oct 24 15:13:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000222.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000222.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-75-6212-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-75-6212-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6212-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000222.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.68 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-75-6212-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-75-6212-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-75-6212-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-75-6212-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4390616: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000223> was used as the working directory.
Started at Wed Oct 24 15:13:32 2012
Results reported at Wed Oct 24 15:13:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000223.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000223.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-80-5611-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-80-5611-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-80-5611-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000223.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.46 sec.
    Max Memory :        10 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-80-5611-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-80-5611-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-80-5611-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-80-5611-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1699>
Subject: Job 4390622: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000224> was used as the working directory.
Started at Wed Oct 24 15:13:32 2012
Results reported at Wed Oct 24 15:13:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000224.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000224.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-86-6562-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-86-6562-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-86-6562-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000224.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.79 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-86-6562-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-86-6562-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-86-6562-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-86-6562-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4390628: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000225> was used as the working directory.
Started at Wed Oct 24 15:13:32 2012
Results reported at Wed Oct 24 15:13:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000225.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000225.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-91-6828-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-91-6828-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6828-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000225.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.50 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6828-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-91-6828-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-91-6828-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-91-6828-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1729>
Subject: Job 4390635: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1729>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000226> was used as the working directory.
Started at Wed Oct 24 15:13:32 2012
Results reported at Wed Oct 24 15:13:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000226.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000226.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-91-6829-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-91-6829-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6829-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000226.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.31 sec.
    Max Memory :        11 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6829-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-91-6829-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-91-6829-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-91-6829-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4390643: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000227> was used as the working directory.
Started at Wed Oct 24 15:13:41 2012
Results reported at Wed Oct 24 15:13:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000227.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000227.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-91-6831-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-91-6831-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6831-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000227.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.80 sec.
    Max Memory :         7 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6831-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-91-6831-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-91-6831-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-91-6831-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4390651: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000228> was used as the working directory.
Started at Wed Oct 24 15:13:43 2012
Results reported at Wed Oct 24 15:14:02 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000228.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000228.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-91-6835-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-91-6835-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6835-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000228.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.98 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6835-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-91-6835-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-91-6835-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-91-6835-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1707>
Subject: Job 4390659: <scatter_215347> Done

Job <scatter_215347> was submitted from host <node1345> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1707>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000229> was used as the working directory.
Started at Wed Oct 24 15:13:51 2012
Results reported at Wed Oct 24 15:14:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000229.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000229.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUAD-91-6836-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUAD-91-6836-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6836-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215347/iteration1/scatter.0000000229.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.73 sec.
    Max Memory :         4 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/luad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUAD.IlluminaGA_DNASeq.Level_2.2.8.0/TCGA-91-6836-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34949878
Writing coverage FWB file LUAD-91-6836-TP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: LUAD-91-6836-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: LUAD-91-6836-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

*** Scatter stdandard err:
*** Scatter retry log:
==> scatter.0000000001.tries <==
1
==> scatter.0000000002.tries <==
1
==> scatter.0000000003.tries <==
1
==> scatter.0000000004.tries <==
1
==> scatter.0000000005.tries <==
1
==> scatter.0000000006.tries <==
1
==> scatter.0000000007.tries <==
1
==> scatter.0000000008.tries <==
1
==> scatter.0000000009.tries <==
1
==> scatter.0000000010.tries <==
1
==> scatter.0000000011.tries <==
1
==> scatter.0000000012.tries <==
1
==> scatter.0000000013.tries <==
1
==> scatter.0000000014.tries <==
1
==> scatter.0000000015.tries <==
1
==> scatter.0000000016.tries <==
1
==> scatter.0000000017.tries <==
1
==> scatter.0000000018.tries <==
1
==> scatter.0000000019.tries <==
1
==> scatter.0000000020.tries <==
1
==> scatter.0000000021.tries <==
1
==> scatter.0000000022.tries <==
1
==> scatter.0000000023.tries <==
1
==> scatter.0000000024.tries <==
1
==> scatter.0000000025.tries <==
1
==> scatter.0000000026.tries <==
1
==> scatter.0000000027.tries <==
1
==> scatter.0000000028.tries <==
1
==> scatter.0000000029.tries <==
1
==> scatter.0000000030.tries <==
1
==> scatter.0000000031.tries <==
1
==> scatter.0000000032.tries <==
1
==> scatter.0000000033.tries <==
1
==> scatter.0000000034.tries <==
1
==> scatter.0000000035.tries <==
1
==> scatter.0000000036.tries <==
1
==> scatter.0000000037.tries <==
1
==> scatter.0000000038.tries <==
1
==> scatter.0000000039.tries <==
1
==> scatter.0000000040.tries <==
1
==> scatter.0000000041.tries <==
1
==> scatter.0000000042.tries <==
1
==> scatter.0000000043.tries <==
1
==> scatter.0000000044.tries <==
1
==> scatter.0000000045.tries <==
1
==> scatter.0000000046.tries <==
1
==> scatter.0000000047.tries <==
1
==> scatter.0000000048.tries <==
1
==> scatter.0000000049.tries <==
1
==> scatter.0000000050.tries <==
1
==> scatter.0000000051.tries <==
1
==> scatter.0000000052.tries <==
1
==> scatter.0000000053.tries <==
1
==> scatter.0000000054.tries <==
1
==> scatter.0000000055.tries <==
1
==> scatter.0000000056.tries <==
1
==> scatter.0000000057.tries <==
1
==> scatter.0000000058.tries <==
1
==> scatter.0000000059.tries <==
1
==> scatter.0000000060.tries <==
1
==> scatter.0000000061.tries <==
1
==> scatter.0000000062.tries <==
1
==> scatter.0000000063.tries <==
1
==> scatter.0000000064.tries <==
1
==> scatter.0000000065.tries <==
1
==> scatter.0000000066.tries <==
1
==> scatter.0000000067.tries <==
1
==> scatter.0000000068.tries <==
1
==> scatter.0000000069.tries <==
1
==> scatter.0000000070.tries <==
1
==> scatter.0000000071.tries <==
1
==> scatter.0000000072.tries <==
1
==> scatter.0000000073.tries <==
1
==> scatter.0000000074.tries <==
1
==> scatter.0000000075.tries <==
1
==> scatter.0000000076.tries <==
1
==> scatter.0000000077.tries <==
1
==> scatter.0000000078.tries <==
1
==> scatter.0000000079.tries <==
1
==> scatter.0000000080.tries <==
1
==> scatter.0000000081.tries <==
1
==> scatter.0000000082.tries <==
1
==> scatter.0000000083.tries <==
1
==> scatter.0000000084.tries <==
1
==> scatter.0000000085.tries <==
1
==> scatter.0000000086.tries <==
1
==> scatter.0000000087.tries <==
1
==> scatter.0000000088.tries <==
1
==> scatter.0000000089.tries <==
1
==> scatter.0000000090.tries <==
1
==> scatter.0000000091.tries <==
1
==> scatter.0000000092.tries <==
1
==> scatter.0000000093.tries <==
1
==> scatter.0000000094.tries <==
1
==> scatter.0000000095.tries <==
1
==> scatter.0000000096.tries <==
1
==> scatter.0000000097.tries <==
1
==> scatter.0000000098.tries <==
1
==> scatter.0000000099.tries <==
1
==> scatter.0000000100.tries <==
1
==> scatter.0000000101.tries <==
1
==> scatter.0000000102.tries <==
1
==> scatter.0000000103.tries <==
1
==> scatter.0000000104.tries <==
1
==> scatter.0000000105.tries <==
1
==> scatter.0000000106.tries <==
1
==> scatter.0000000107.tries <==
1
==> scatter.0000000108.tries <==
1
==> scatter.0000000109.tries <==
1
==> scatter.0000000110.tries <==
1
==> scatter.0000000111.tries <==
1
==> scatter.0000000112.tries <==
1
==> scatter.0000000113.tries <==
1
==> scatter.0000000114.tries <==
1
==> scatter.0000000115.tries <==
1
==> scatter.0000000116.tries <==
1
==> scatter.0000000117.tries <==
1
==> scatter.0000000118.tries <==
1
==> scatter.0000000119.tries <==
1
==> scatter.0000000120.tries <==
1
==> scatter.0000000121.tries <==
1
==> scatter.0000000122.tries <==
1
==> scatter.0000000123.tries <==
1
==> scatter.0000000124.tries <==
1
==> scatter.0000000125.tries <==
1
==> scatter.0000000126.tries <==
1
==> scatter.0000000127.tries <==
1
==> scatter.0000000128.tries <==
1
==> scatter.0000000129.tries <==
1
==> scatter.0000000130.tries <==
1
==> scatter.0000000131.tries <==
1
==> scatter.0000000132.tries <==
1
==> scatter.0000000133.tries <==
1
==> scatter.0000000134.tries <==
1
==> scatter.0000000135.tries <==
1
==> scatter.0000000136.tries <==
1
==> scatter.0000000137.tries <==
1
==> scatter.0000000138.tries <==
1
==> scatter.0000000139.tries <==
1
==> scatter.0000000140.tries <==
1
==> scatter.0000000141.tries <==
1
==> scatter.0000000142.tries <==
1
==> scatter.0000000143.tries <==
1
==> scatter.0000000144.tries <==
1
==> scatter.0000000145.tries <==
1
==> scatter.0000000146.tries <==
1
==> scatter.0000000147.tries <==
1
==> scatter.0000000148.tries <==
1
==> scatter.0000000149.tries <==
1
==> scatter.0000000150.tries <==
1
==> scatter.0000000151.tries <==
1
==> scatter.0000000152.tries <==
1
==> scatter.0000000153.tries <==
1
==> scatter.0000000154.tries <==
1
==> scatter.0000000155.tries <==
1
==> scatter.0000000156.tries <==
1
==> scatter.0000000157.tries <==
1
==> scatter.0000000158.tries <==
1
==> scatter.0000000159.tries <==
1
==> scatter.0000000160.tries <==
1
==> scatter.0000000161.tries <==
1
==> scatter.0000000162.tries <==
1
==> scatter.0000000163.tries <==
1
==> scatter.0000000164.tries <==
1
==> scatter.0000000165.tries <==
1
==> scatter.0000000166.tries <==
1
==> scatter.0000000167.tries <==
1
==> scatter.0000000168.tries <==
1
==> scatter.0000000169.tries <==
1
==> scatter.0000000170.tries <==
1
==> scatter.0000000171.tries <==
1
==> scatter.0000000172.tries <==
1
==> scatter.0000000173.tries <==
1
==> scatter.0000000174.tries <==
1
==> scatter.0000000175.tries <==
1
==> scatter.0000000176.tries <==
1
==> scatter.0000000177.tries <==
1
==> scatter.0000000178.tries <==
1
==> scatter.0000000179.tries <==
1
==> scatter.0000000180.tries <==
1
==> scatter.0000000181.tries <==
1
==> scatter.0000000182.tries <==
1
==> scatter.0000000183.tries <==
1
==> scatter.0000000184.tries <==
1
==> scatter.0000000185.tries <==
1
==> scatter.0000000186.tries <==
1
==> scatter.0000000187.tries <==
1
==> scatter.0000000188.tries <==
1
==> scatter.0000000189.tries <==
1
==> scatter.0000000190.tries <==
1
==> scatter.0000000191.tries <==
1
==> scatter.0000000192.tries <==
1
==> scatter.0000000193.tries <==
1
==> scatter.0000000194.tries <==
1
==> scatter.0000000195.tries <==
1
==> scatter.0000000196.tries <==
1
==> scatter.0000000197.tries <==
1
==> scatter.0000000198.tries <==
1
==> scatter.0000000199.tries <==
1
==> scatter.0000000200.tries <==
1
==> scatter.0000000201.tries <==
1
==> scatter.0000000202.tries <==
1
==> scatter.0000000203.tries <==
1
==> scatter.0000000204.tries <==
1
==> scatter.0000000205.tries <==
1
==> scatter.0000000206.tries <==
1
==> scatter.0000000207.tries <==
1
==> scatter.0000000208.tries <==
1
==> scatter.0000000209.tries <==
1
==> scatter.0000000210.tries <==
1
==> scatter.0000000211.tries <==
1
==> scatter.0000000212.tries <==
1
==> scatter.0000000213.tries <==
1
==> scatter.0000000214.tries <==
1
==> scatter.0000000215.tries <==
1
==> scatter.0000000216.tries <==
1
==> scatter.0000000217.tries <==
1
==> scatter.0000000218.tries <==
1
==> scatter.0000000219.tries <==
1
==> scatter.0000000220.tries <==
1
==> scatter.0000000221.tries <==
1
==> scatter.0000000222.tries <==
1
==> scatter.0000000223.tries <==
1
==> scatter.0000000224.tries <==
1
==> scatter.0000000225.tries <==
1
==> scatter.0000000226.tries <==
1
==> scatter.0000000227.tries <==
1
==> scatter.0000000228.tries <==
1
==> scatter.0000000229.tries <==
1


PS:

Read file <scatter-gather.err.txt> for stderr output of this job.

*** Scatter Gather stdandard err:
ls: iteration1/sg-next-iteration.txt: No such file or directory


PS:

Read file <iterator.err.txt> for stderr output of this job.

