Sender: LSF System <lsf@node1541>
Subject: Job 4403037: <iteration_216151> Done

Job <iteration_216151> was submitted from host <node1719> 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/216151> was used as the working directory.
Started at Wed Oct 24 16:50:44 2012
Results reported at Wed Oct 24 16:50:47 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 ${return_code} > exited;
exit 1;
fi
/xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 216151 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
return_code=$?
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/216151
rmdir iteration*
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :      0.80 sec.
    Max Memory :         3 MB
    Max Swap   :        39 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 216151 --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@node1726>
Subject: Job 4403031: <gather_216151> Done

Job <gather_216151> was submitted from host <node1719> 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/216151/iteration1> was used as the working directory.
Started at Wed Oct 24 16:35:59 2012
Results reported at Wed Oct 24 16:50:37 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 83 ]; 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/" "PRAD" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/PRAD/1910971/0.MutSigPreprocess.Finished/PRAD.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/PRAD/1910971/0.MutSigPreprocess.Finished/PRAD.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   :    858.20 sec.
    Max Memory :      6881 MB
    Max Swap   :      8317 MB

    Max Processes  :         6
    Max Threads    :        64

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
83 files found
83 files found
83 files found
Creating summed FWB coverage file: ./PRAD.summed_coverage.fwb
Loading target file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Opening files: 10/83 20/83 30/83 40/83 50/83 60/83 70/83 80/83 
Summing and writing output file:
1/4283949 Elapsed time is 0.001478 seconds.
100001/4283949 Elapsed time is 1.714795 seconds.
200001/4283949 Elapsed time is 2.638752 seconds.
300001/4283949 Elapsed time is 2.787974 seconds.
400001/4283949 Elapsed time is 2.934690 seconds.
500001/4283949 Elapsed time is 3.106968 seconds.
600001/4283949 Elapsed time is 3.251076 seconds.
700001/4283949 Elapsed time is 3.397486 seconds.
800001/4283949 Elapsed time is 3.547510 seconds.
900001/4283949 Elapsed time is 3.695563 seconds.
1000001/4283949 Elapsed time is 4.078735 seconds.
1100001/4283949 Elapsed time is 4.228213 seconds.
1200001/4283949 Elapsed time is 4.373357 seconds.
1300001/4283949 Elapsed time is 4.520884 seconds.
1400001/4283949 Elapsed time is 4.668758 seconds.
1500001/4283949 Elapsed time is 4.816834 seconds.
1600001/4283949 Elapsed time is 4.964902 seconds.
1700001/4283949 Elapsed time is 5.112442 seconds.
1800001/4283949 Elapsed time is 5.258080 seconds.
1900001/4283949 Elapsed time is 5.408451 seconds.
2000001/4283949 Elapsed time is 5.555165 seconds.
2100001/4283949 Elapsed time is 5.709296 seconds.
2200001/4283949 Elapsed time is 5.856599 seconds.
2300001/4283949 Elapsed time is 6.004404 seconds.
2400001/4283949 Elapsed time is 6.153266 seconds.
2500001/4283949 Elapsed time is 6.301536 seconds.
2600001/4283949 Elapsed time is 6.452102 seconds.
2700001/4283949 Elapsed time is 6.601346 seconds.
2800001/4283949 Elapsed time is 6.748959 seconds.
2900001/4283949 Elapsed time is 6.896979 seconds.
3000001/4283949 Elapsed time is 7.044928 seconds.
3100001/4283949 Elapsed time is 7.193552 seconds.
3200001/4283949 Elapsed time is 7.342581 seconds.
3300001/4283949 Elapsed time is 7.492975 seconds.
3400001/4283949 Elapsed time is 7.651078 seconds.
3500001/4283949 Elapsed time is 7.804318 seconds.
3600001/4283949 Elapsed time is 7.954692 seconds.
3700001/4283949 Elapsed time is 8.108967 seconds.
3800001/4283949 Elapsed time is 8.260317 seconds.
3900001/4283949 Elapsed time is 8.412244 seconds.
4000001/4283949 Elapsed time is 8.564551 seconds.
4100001/4283949 Elapsed time is 8.714480 seconds.
4200001/4283949 Elapsed time is 8.867585 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  5213 N 7477779447  rate 6.97e-07 (1.00x)  ci 6.78e-07 to 7.16e-07

k=2
                  transit   n  3205 N 2492593149  rate 1.29e-06 (1.84x)  ci 1.24e-06 to 1.33e-06
                 transver   n  2008 N 4985186298  rate 4.03e-07 (0.58x)  ci 3.85e-07 to 4.21e-07

k=3
                *CpG->mut   n  1679 N  417494949  rate 4.02e-06 (5.77x)  ci 3.83e-06 to 4.22e-06
          *Cp(A/C/T)->mut   n  2048 N 3398564028  rate 6.03e-07 (0.86x)  ci 5.77e-07 to 6.29e-07
                   A->mut   n  1486 N 3661720470  rate 4.06e-07 (0.58x)  ci 3.85e-07 to 4.27e-07

k=4
                  *CpG->T   n  1409 N  139164983  rate 1.01e-05 (14.5x)  ci 9.60e-06 to 1.07e-05
      *Np(A/C/T)->transit   n  1574 N 1971062625  rate 7.99e-07 (1.15x)  ci 7.60e-07 to 8.39e-07
                  *ApG->G   n   222 N  382365541  rate 5.81e-07 (0.83x)  ci 5.07e-07 to 6.62e-07
                 transver   n  2008 N 4985186298  rate 4.03e-07 (0.58x)  ci 3.85e-07 to 4.21e-07

Saving ./PRAD.mutcategs.txt
all files are *.bin: will read in BINARY MODE
83 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 137086340: appears to include noncoding areas
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Saving ./PRAD.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/216151/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/ PRAD /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/PRAD/1910971/0.MutSigPreprocess.Finished/PRAD.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/PRAD/1910971/0.MutSigPreprocess.Finished/PRAD.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@node1529>
Subject: Job 4402507: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000001> was used as the working directory.
Started at Wed Oct 24 15:49:23 2012
Results reported at Wed Oct 24 16:34:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000001.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5737-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5737-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5737-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :    151.06 sec.
    Max Memory :      4734 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5737-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=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=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35907894
Writing coverage FWB file PRAD-CH-5737-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: PRAD-CH-5737-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5737-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 4402512: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000002> was used as the working directory.
Started at Wed Oct 24 15:49:43 2012
Results reported at Wed Oct 24 15:50:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000002.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5738-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5738-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5738-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     35.73 sec.
    Max Memory :      4716 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5738-01.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=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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 36090036
Writing coverage FWB file PRAD-CH-5738-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: PRAD-CH-5738-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5738-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 4402515: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000003> was used as the working directory.
Started at Wed Oct 24 15:50:31 2012
Results reported at Wed Oct 24 15:50:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000003.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5739-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5739-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5739-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.91 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5739-01.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=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
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

  Total coverage = 35298522
Writing coverage FWB file PRAD-CH-5739-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: PRAD-CH-5739-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5739-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 4402521: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000004> was used as the working directory.
Started at Wed Oct 24 15:51:47 2012
Results reported at Wed Oct 24 15:52:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000004.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5740-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5740-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5740-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     36.57 sec.
    Max Memory :      4733 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5740-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 35723391
Writing coverage FWB file PRAD-CH-5740-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: PRAD-CH-5740-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5740-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 4402525: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000005> was used as the working directory.
Started at Wed Oct 24 15:53:10 2012
Results reported at Wed Oct 24 16:35:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000005.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5741-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5741-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5741-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     22.08 sec.
    Max Memory :      4739 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5741-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
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 = 35816482
Writing coverage FWB file PRAD-CH-5741-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: PRAD-CH-5741-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5741-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 4402529: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000006> was used as the working directory.
Started at Wed Oct 24 15:53:37 2012
Results reported at Wed Oct 24 15:53:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000006.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5743-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5743-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5743-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.77 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5743-01.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=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000228.1
Ignoring chrom=GL000228.1
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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35580790
Writing coverage FWB file PRAD-CH-5743-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: PRAD-CH-5743-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5743-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 4402535: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000007> was used as the working directory.
Started at Wed Oct 24 15:55:02 2012
Results reported at Wed Oct 24 15:56:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000007.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5744-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5744-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5744-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     41.94 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5744-01.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=GL000201.1
Ignoring chrom=GL000241.1
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=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=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=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=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=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=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=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

  Total coverage = 35975188
Writing coverage FWB file PRAD-CH-5744-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: PRAD-CH-5744-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5744-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 4402540: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000008> was used as the working directory.
Started at Wed Oct 24 15:55:12 2012
Results reported at Wed Oct 24 15:55:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000008.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5745-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5745-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5745-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.90 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5745-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=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=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 36035495
Writing coverage FWB file PRAD-CH-5745-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: PRAD-CH-5745-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5745-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1423>
Subject: Job 4402544: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1423>, 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/216151/iteration1/scatter.0000000009> was used as the working directory.
Started at Wed Oct 24 15:55:33 2012
Results reported at Wed Oct 24 15:56:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000009.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5746-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5746-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5746-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     34.42 sec.
    Max Memory :      4721 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5746-01.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=GL000241.1
Ignoring chrom=GL000241.1
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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=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=GL000222.1
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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35343806
Writing coverage FWB file PRAD-CH-5746-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: PRAD-CH-5746-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5746-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 4402549: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000010> was used as the working directory.
Started at Wed Oct 24 15:55:53 2012
Results reported at Wed Oct 24 15:56:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000010.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5748-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5748-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5748-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     36.46 sec.
    Max Memory :      4726 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5748-01.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=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=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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 35755357
Writing coverage FWB file PRAD-CH-5748-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: PRAD-CH-5748-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5748-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1423>
Subject: Job 4402555: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1423>, 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/216151/iteration1/scatter.0000000011> was used as the working directory.
Started at Wed Oct 24 15:56:33 2012
Results reported at Wed Oct 24 15:57:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000011.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5750-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5750-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5750-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     33.78 sec.
    Max Memory :      4734 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5750-01.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=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=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000212.1
Ignoring chrom=GL000212.1
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=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=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=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

  Total coverage = 36092166
Writing coverage FWB file PRAD-CH-5750-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: PRAD-CH-5750-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5750-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1530>
Subject: Job 4402561: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1530>, 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/216151/iteration1/scatter.0000000012> was used as the working directory.
Started at Wed Oct 24 15:57:35 2012
Results reported at Wed Oct 24 15:58:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000012.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5751-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5751-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5751-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     31.90 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5751-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=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=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=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=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

  Total coverage = 36249700
Writing coverage FWB file PRAD-CH-5751-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: PRAD-CH-5751-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5751-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 4402567: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000013> was used as the working directory.
Started at Wed Oct 24 15:58:04 2012
Results reported at Wed Oct 24 15:58:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000013.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5752-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5752-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5752-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     32.39 sec.
    Max Memory :      4724 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5752-01.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=GL000241.1
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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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 = 35511012
Writing coverage FWB file PRAD-CH-5752-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: PRAD-CH-5752-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5752-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1547>
Subject: Job 4402571: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, 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/216151/iteration1/scatter.0000000014> was used as the working directory.
Started at Wed Oct 24 15:58:18 2012
Results reported at Wed Oct 24 15:58:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000014.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5753-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5753-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5753-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     31.66 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5753-01.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=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=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35649893
Writing coverage FWB file PRAD-CH-5753-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: PRAD-CH-5753-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5753-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 4402576: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000015> was used as the working directory.
Started at Wed Oct 24 15:58:49 2012
Results reported at Wed Oct 24 15:59:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000015.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5754-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5754-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5754-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     35.79 sec.
    Max Memory :      4744 MB
    Max Swap   :      5469 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5754-01.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=GL000201.1
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=GL000209.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=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=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
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 = 36260880
Writing coverage FWB file PRAD-CH-5754-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: PRAD-CH-5754-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5754-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 4402582: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000016> was used as the working directory.
Started at Wed Oct 24 15:59:29 2012
Results reported at Wed Oct 24 15:59:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000016.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5761-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5761-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5761-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.94 sec.
    Max Memory :         7 MB
    Max Swap   :        49 MB

    Max Processes  :         2
    Max Threads    :         2

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5761-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35618728
Writing coverage FWB file PRAD-CH-5761-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: PRAD-CH-5761-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5761-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1640>
Subject: Job 4402585: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, 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/216151/iteration1/scatter.0000000017> was used as the working directory.
Started at Wed Oct 24 15:59:45 2012
Results reported at Wed Oct 24 16:00:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000017.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5762-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5762-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5762-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.63 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5762-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
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=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35647898
Writing coverage FWB file PRAD-CH-5762-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: PRAD-CH-5762-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5762-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 4402592: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000018> was used as the working directory.
Started at Wed Oct 24 16:01:41 2012
Results reported at Wed Oct 24 16:02:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000018.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5763-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5763-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5763-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     30.77 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5763-01.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=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=GL000237.1
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=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35356061
Writing coverage FWB file PRAD-CH-5763-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: PRAD-CH-5763-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5763-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 4402597: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000019> was used as the working directory.
Started at Wed Oct 24 16:02:44 2012
Results reported at Wed Oct 24 16:03:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000019.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5764-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5764-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5764-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     29.85 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5764-01.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=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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35780287
Writing coverage FWB file PRAD-CH-5764-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: PRAD-CH-5764-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5764-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 4402603: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000020> was used as the working directory.
Started at Wed Oct 24 16:02:44 2012
Results reported at Wed Oct 24 16:03:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000020.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5765-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5765-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5765-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     31.96 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5765-01.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=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
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=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35286941
Writing coverage FWB file PRAD-CH-5765-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: PRAD-CH-5765-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5765-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 4402608: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000021> was used as the working directory.
Started at Wed Oct 24 16:02:44 2012
Results reported at Wed Oct 24 16:03:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000021.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5766-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5766-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5766-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     36.64 sec.
    Max Memory :      4709 MB
    Max Swap   :      5457 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5766-01.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=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=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=GL000228.1
Ignoring chrom=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 36332406
Writing coverage FWB file PRAD-CH-5766-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: PRAD-CH-5766-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5766-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1652>
Subject: Job 4402614: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1652>, 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/216151/iteration1/scatter.0000000022> was used as the working directory.
Started at Wed Oct 24 16:03:02 2012
Results reported at Wed Oct 24 16:06:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000022.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5767-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5767-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5767-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     19.40 sec.
    Max Memory :      4440 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5767-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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 = 34043667
Writing coverage FWB file PRAD-CH-5767-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: PRAD-CH-5767-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5767-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 4402619: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000023> was used as the working directory.
Started at Wed Oct 24 16:03:14 2012
Results reported at Wed Oct 24 16:03:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000023.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5768-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5768-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5768-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.55 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5768-01.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=GL000237.1
Ignoring chrom=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000214.1
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=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=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35069093
Writing coverage FWB file PRAD-CH-5768-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: PRAD-CH-5768-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5768-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 4402624: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000024> was used as the working directory.
Started at Wed Oct 24 16:03:37 2012
Results reported at Wed Oct 24 16:04:02 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000024.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5769-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5769-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5769-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.30 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5769-01.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=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=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=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=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=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=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=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1

  Total coverage = 35036222
Writing coverage FWB file PRAD-CH-5769-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: PRAD-CH-5769-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5769-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 4402663: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000025> was used as the working directory.
Started at Wed Oct 24 16:03:44 2012
Results reported at Wed Oct 24 16:04:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000025.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5771-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5771-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5771-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     18.35 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5771-01.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=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=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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=GL000193.1
Ignoring chrom=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=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 35824074
Writing coverage FWB file PRAD-CH-5771-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: PRAD-CH-5771-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5771-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1428>
Subject: Job 4402666: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1428>, 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/216151/iteration1/scatter.0000000026> was used as the working directory.
Started at Wed Oct 24 16:04:02 2012
Results reported at Wed Oct 24 16:04:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000026.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5772-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5772-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5772-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     31.79 sec.
    Max Memory :      4743 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5772-01.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=GL000201.1
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=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=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=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=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=GL000222.1
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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 36285737
Writing coverage FWB file PRAD-CH-5772-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: PRAD-CH-5772-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5772-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1547>
Subject: Job 4402670: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, 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/216151/iteration1/scatter.0000000027> was used as the working directory.
Started at Wed Oct 24 16:04:21 2012
Results reported at Wed Oct 24 16:04:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000027.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5788-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5788-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5788-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     28.65 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5788-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35785760
Writing coverage FWB file PRAD-CH-5788-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: PRAD-CH-5788-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5788-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 4402674: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000028> was used as the working directory.
Started at Wed Oct 24 16:04:21 2012
Results reported at Wed Oct 24 16:04:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000028.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5789-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5789-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5789-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     21.12 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5789-01.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=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=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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=GL000222.1
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=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=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 35991882
Writing coverage FWB file PRAD-CH-5789-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: PRAD-CH-5789-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5789-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1650>
Subject: Job 4402721: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1650>, 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/216151/iteration1/scatter.0000000029> was used as the working directory.
Started at Wed Oct 24 16:04:29 2012
Results reported at Wed Oct 24 16:04:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000029.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5790-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5790-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5790-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     19.30 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5790-01.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=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=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=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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=GL000222.1
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=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=GL000193.1
Ignoring chrom=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=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 35575407
Writing coverage FWB file PRAD-CH-5790-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: PRAD-CH-5790-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5790-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 4402728: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000030> was used as the working directory.
Started at Wed Oct 24 16:04:37 2012
Results reported at Wed Oct 24 16:06:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000030.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5791-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5791-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5791-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     48.17 sec.
    Max Memory :      4716 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5791-01.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=GL000241.1
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=GL000243.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35501927
Writing coverage FWB file PRAD-CH-5791-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: PRAD-CH-5791-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5791-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1530>
Subject: Job 4402737: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1530>, 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/216151/iteration1/scatter.0000000031> was used as the working directory.
Started at Wed Oct 24 16:04:37 2012
Results reported at Wed Oct 24 16:05:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000031.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5792-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5792-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5792-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     29.57 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5792-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=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=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 35518049
Writing coverage FWB file PRAD-CH-5792-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: PRAD-CH-5792-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5792-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1425>
Subject: Job 4402742: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1425>, 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/216151/iteration1/scatter.0000000032> was used as the working directory.
Started at Wed Oct 24 16:05:06 2012
Results reported at Wed Oct 24 16:05:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000032.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-CH-5794-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-CH-5794-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5794-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     32.38 sec.
    Max Memory :      4732 MB
    Max Swap   :      5519 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CH-5794-01.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=GL000241.1
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=GL000237.1
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=GL000204.1
Ignoring chrom=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000222.1
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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34889318
Writing coverage FWB file PRAD-CH-5794-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: PRAD-CH-5794-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-CH-5794-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 4402748: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000033> was used as the working directory.
Started at Wed Oct 24 16:05:50 2012
Results reported at Wed Oct 24 16:06:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000033.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5494-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5494-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5494-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     32.35 sec.
    Max Memory :      4713 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5494-01.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=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=GL000241.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=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=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

  Total coverage = 35272869
Writing coverage FWB file PRAD-EJ-5494-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: PRAD-EJ-5494-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5494-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 4402754: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000034> was used as the working directory.
Started at Wed Oct 24 16:05:50 2012
Results reported at Wed Oct 24 16:06:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000034.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5495-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5495-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5495-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.76 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5495-01.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=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=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 36387040
Writing coverage FWB file PRAD-EJ-5495-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: PRAD-EJ-5495-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5495-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 4402759: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000035> was used as the working directory.
Started at Wed Oct 24 16:05:59 2012
Results reported at Wed Oct 24 16:06:20 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000035.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5496-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5496-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5496-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.07 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5496-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000214.1
Ignoring chrom=GL000214.1
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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000222.1
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=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

  Total coverage = 35836329
Writing coverage FWB file PRAD-EJ-5496-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: PRAD-EJ-5496-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5496-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 4402762: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000036> was used as the working directory.
Started at Wed Oct 24 16:06:40 2012
Results reported at Wed Oct 24 16:07:02 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000036.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5497-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5497-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5497-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.18 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5497-01.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=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=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=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
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 = 35665951
Writing coverage FWB file PRAD-EJ-5497-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: PRAD-EJ-5497-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5497-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 4402770: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000037> was used as the working directory.
Started at Wed Oct 24 16:06:56 2012
Results reported at Wed Oct 24 16:07:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000037.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5498-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5498-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5498-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     30.22 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5498-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 35799907
Writing coverage FWB file PRAD-EJ-5498-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: PRAD-EJ-5498-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5498-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 4402774: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000038> was used as the working directory.
Started at Wed Oct 24 16:06:56 2012
Results reported at Wed Oct 24 16:07:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000038.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5499-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5499-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5499-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.35 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5499-01.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=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=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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=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=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 35688512
Writing coverage FWB file PRAD-EJ-5499-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: PRAD-EJ-5499-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5499-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 4402780: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000039> was used as the working directory.
Started at Wed Oct 24 16:06:59 2012
Results reported at Wed Oct 24 16:11:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000039.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5501-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5501-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5501-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     62.22 sec.
    Max Memory :      4732 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5501-01.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=GL000201.1
Ignoring chrom=GL000201.1
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=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=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=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=GL000209.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000195.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=GL000193.1
Ignoring chrom=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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 = 35488078
Writing coverage FWB file PRAD-EJ-5501-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: PRAD-EJ-5501-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5501-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4402785: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, 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/216151/iteration1/scatter.0000000040> was used as the working directory.
Started at Wed Oct 24 16:06:59 2012
Results reported at Wed Oct 24 16:07:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000040.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5502-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5502-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5502-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.11 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5502-01.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=GL000241.1
Ignoring chrom=GL000241.1
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=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=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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 = 35297086
Writing coverage FWB file PRAD-EJ-5502-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: PRAD-EJ-5502-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5502-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 4402790: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000041> was used as the working directory.
Started at Wed Oct 24 16:07:22 2012
Results reported at Wed Oct 24 16:07:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000041.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5503-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5503-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5503-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     31.32 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5503-01.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=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=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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35522299
Writing coverage FWB file PRAD-EJ-5503-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: PRAD-EJ-5503-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5503-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1547>
Subject: Job 4402796: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, 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/216151/iteration1/scatter.0000000042> was used as the working directory.
Started at Wed Oct 24 16:07:26 2012
Results reported at Wed Oct 24 16:07:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000042.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5504-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5504-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5504-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     31.75 sec.
    Max Memory :      4741 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5504-01.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=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=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=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=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=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000212.1
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=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=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=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 36143788
Writing coverage FWB file PRAD-EJ-5504-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: PRAD-EJ-5504-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5504-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 4402803: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000043> was used as the working directory.
Started at Wed Oct 24 16:07:26 2012
Results reported at Wed Oct 24 16:08:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000043.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5505-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5505-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5505-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     35.08 sec.
    Max Memory :      4720 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5505-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000221.1
Ignoring chrom=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=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=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=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=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=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
Ignoring chrom=GL000192.1

  Total coverage = 35746557
Writing coverage FWB file PRAD-EJ-5505-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: PRAD-EJ-5505-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5505-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1530>
Subject: Job 4402812: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1530>, 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/216151/iteration1/scatter.0000000044> was used as the working directory.
Started at Wed Oct 24 16:07:52 2012
Results reported at Wed Oct 24 16:08:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000044.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5506-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5506-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5506-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     33.33 sec.
    Max Memory :      4729 MB
    Max Swap   :      5457 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5506-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=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=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 35956642
Writing coverage FWB file PRAD-EJ-5506-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: PRAD-EJ-5506-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5506-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4402820: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, 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/216151/iteration1/scatter.0000000045> was used as the working directory.
Started at Wed Oct 24 16:08:02 2012
Results reported at Wed Oct 24 16:08:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000045.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5507-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5507-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5507-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     15.81 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5507-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35560444
Writing coverage FWB file PRAD-EJ-5507-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: PRAD-EJ-5507-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5507-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 4402827: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000046> was used as the working directory.
Started at Wed Oct 24 16:08:02 2012
Results reported at Wed Oct 24 16:08:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000046.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5508-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5508-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5508-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     28.38 sec.
    Max Memory :      4741 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5508-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000214.1
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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000222.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35759783
Writing coverage FWB file PRAD-EJ-5508-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: PRAD-EJ-5508-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5508-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 4402832: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000047> was used as the working directory.
Started at Wed Oct 24 16:08:22 2012
Results reported at Wed Oct 24 16:08:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000047.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5509-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5509-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5509-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     32.35 sec.
    Max Memory :      4716 MB
    Max Swap   :      5454 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5509-01.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=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=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
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=GL000219.1
Ignoring chrom=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=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=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=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=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

  Total coverage = 34543789
Writing coverage FWB file PRAD-EJ-5509-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: PRAD-EJ-5509-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5509-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4402839: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, 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/216151/iteration1/scatter.0000000048> was used as the working directory.
Started at Wed Oct 24 16:09:02 2012
Results reported at Wed Oct 24 16:09:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000048.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5510-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5510-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5510-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.36 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5510-01.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=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=GL000243.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=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=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=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=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 35331349
Writing coverage FWB file PRAD-EJ-5510-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: PRAD-EJ-5510-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5510-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 4402848: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000049> was used as the working directory.
Started at Wed Oct 24 16:09:23 2012
Results reported at Wed Oct 24 16:09:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000049.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5511-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5511-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5511-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     30.78 sec.
    Max Memory :      4721 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5511-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
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=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=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35221112
Writing coverage FWB file PRAD-EJ-5511-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: PRAD-EJ-5511-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5511-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4402854: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, 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/216151/iteration1/scatter.0000000050> was used as the working directory.
Started at Wed Oct 24 16:10:07 2012
Results reported at Wed Oct 24 16:10:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000050.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5512-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5512-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5512-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.71 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5512-01.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=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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 35843480
Writing coverage FWB file PRAD-EJ-5512-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: PRAD-EJ-5512-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5512-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 4402857: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000051> was used as the working directory.
Started at Wed Oct 24 16:10:14 2012
Results reported at Wed Oct 24 16:10:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000051.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5514-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5514-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5514-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.37 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5514-01.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=GL000241.1
Ignoring chrom=GL000241.1
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=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000227.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35736248
Writing coverage FWB file PRAD-EJ-5514-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: PRAD-EJ-5514-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5514-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 4402860: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000052> was used as the working directory.
Started at Wed Oct 24 16:10:18 2012
Results reported at Wed Oct 24 16:10:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000052.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5515-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5515-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5515-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.69 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5515-01.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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000214.1
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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 33937198
Writing coverage FWB file PRAD-EJ-5515-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: PRAD-EJ-5515-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5515-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 4402866: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000053> was used as the working directory.
Started at Wed Oct 24 16:10:44 2012
Results reported at Wed Oct 24 16:11:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000053.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5516-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5516-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5516-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.28 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5516-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000243.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000221.1
Ignoring chrom=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35950578
Writing coverage FWB file PRAD-EJ-5516-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: PRAD-EJ-5516-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5516-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 4402870: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000054> was used as the working directory.
Started at Wed Oct 24 16:10:50 2012
Results reported at Wed Oct 24 16:11:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000054.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5517-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5517-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5517-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.96 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5517-01.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=GL000241.1
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=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35980079
Writing coverage FWB file PRAD-EJ-5517-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: PRAD-EJ-5517-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5517-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4402876: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, 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/216151/iteration1/scatter.0000000055> was used as the working directory.
Started at Wed Oct 24 16:11:08 2012
Results reported at Wed Oct 24 16:11:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000055.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5518-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5518-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5518-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     18.18 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5518-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=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=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=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000222.1
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=GL000194.1
Ignoring chrom=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

  Total coverage = 34953788
Writing coverage FWB file PRAD-EJ-5518-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: PRAD-EJ-5518-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5518-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 4402883: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000056> was used as the working directory.
Started at Wed Oct 24 16:11:18 2012
Results reported at Wed Oct 24 16:11:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000056.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5519-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5519-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5519-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.40 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5519-01.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=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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=GL000205.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34915032
Writing coverage FWB file PRAD-EJ-5519-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: PRAD-EJ-5519-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5519-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1640>
Subject: Job 4402889: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, 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/216151/iteration1/scatter.0000000057> was used as the working directory.
Started at Wed Oct 24 16:11:28 2012
Results reported at Wed Oct 24 16:11:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000057.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5521-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5521-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5521-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     18.04 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5521-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=GL000237.1
Ignoring chrom=GL000237.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000221.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=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=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34954407
Writing coverage FWB file PRAD-EJ-5521-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: PRAD-EJ-5521-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5521-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 4402893: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000058> was used as the working directory.
Started at Wed Oct 24 16:11:36 2012
Results reported at Wed Oct 24 16:12:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000058.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5522-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5522-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5522-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     32.96 sec.
    Max Memory :      4742 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5522-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35782720
Writing coverage FWB file PRAD-EJ-5522-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: PRAD-EJ-5522-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5522-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 4402898: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000059> was used as the working directory.
Started at Wed Oct 24 16:11:45 2012
Results reported at Wed Oct 24 16:12:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000059.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5524-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5524-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5524-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.21 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5524-01.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=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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
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=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35861207
Writing coverage FWB file PRAD-EJ-5524-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: PRAD-EJ-5524-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5524-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 4402904: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000060> was used as the working directory.
Started at Wed Oct 24 16:11:52 2012
Results reported at Wed Oct 24 16:12:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000060.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5525-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5525-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5525-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.06 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5525-01.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=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000222.1
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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 36218720
Writing coverage FWB file PRAD-EJ-5525-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: PRAD-EJ-5525-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5525-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1429>
Subject: Job 4402907: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1429>, 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/216151/iteration1/scatter.0000000061> was used as the working directory.
Started at Wed Oct 24 16:11:55 2012
Results reported at Wed Oct 24 16:12:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000061.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5526-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5526-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5526-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     31.21 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5526-01.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=GL000241.1
Ignoring chrom=GL000241.1
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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=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=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=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 36006961
Writing coverage FWB file PRAD-EJ-5526-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: PRAD-EJ-5526-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5526-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1640>
Subject: Job 4402914: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, 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/216151/iteration1/scatter.0000000062> was used as the working directory.
Started at Wed Oct 24 16:12:30 2012
Results reported at Wed Oct 24 16:12:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000062.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5527-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5527-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5527-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.75 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5527-01.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=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=GL000222.1
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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 36040095
Writing coverage FWB file PRAD-EJ-5527-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: PRAD-EJ-5527-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5527-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 4402918: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000063> was used as the working directory.
Started at Wed Oct 24 16:12:36 2012
Results reported at Wed Oct 24 16:13:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000063.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5530-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5530-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5530-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     36.46 sec.
    Max Memory :      4714 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5530-01.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=GL000201.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=GL000221.1
Ignoring chrom=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=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=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=GL000222.1
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=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=GL000193.1
Ignoring chrom=GL000193.1
Ignoring chrom=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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 = 35114625
Writing coverage FWB file PRAD-EJ-5530-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: PRAD-EJ-5530-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5530-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 4402924: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000064> was used as the working directory.
Started at Wed Oct 24 16:12:58 2012
Results reported at Wed Oct 24 16:13:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000064.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5531-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5531-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5531-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.26 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5531-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=GL000204.1
Ignoring chrom=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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
Ignoring chrom=GL000212.1
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=GL000222.1
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=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=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=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

  Total coverage = 29778844
Writing coverage FWB file PRAD-EJ-5531-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: PRAD-EJ-5531-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5531-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4402929: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, 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/216151/iteration1/scatter.0000000065> was used as the working directory.
Started at Wed Oct 24 16:13:09 2012
Results reported at Wed Oct 24 16:13:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000065.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5532-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5532-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5532-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.70 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5532-01.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=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=GL000220.1
Ignoring chrom=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34740384
Writing coverage FWB file PRAD-EJ-5532-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: PRAD-EJ-5532-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5532-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 4402935: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000066> was used as the working directory.
Started at Wed Oct 24 16:13:21 2012
Results reported at Wed Oct 24 16:13:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000066.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-EJ-5542-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-EJ-5542-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5542-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EJ-5542-01.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=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=GL000237.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=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=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=GL000212.1
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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35978616
Writing coverage FWB file PRAD-EJ-5542-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: PRAD-EJ-5542-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-EJ-5542-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1640>
Subject: Job 4402941: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, 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/216151/iteration1/scatter.0000000067> was used as the working directory.
Started at Wed Oct 24 16:13:30 2012
Results reported at Wed Oct 24 16:13:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000067.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6332-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6332-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6332-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.54 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6332-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
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=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 31766759
Writing coverage FWB file PRAD-G9-6332-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: PRAD-G9-6332-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6332-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 4402947: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000068> was used as the working directory.
Started at Wed Oct 24 16:13:42 2012
Results reported at Wed Oct 24 16:14:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000068.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6336-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6336-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6336-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     30.23 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6336-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34772021
Writing coverage FWB file PRAD-G9-6336-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: PRAD-G9-6336-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6336-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 4402954: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000069> was used as the working directory.
Started at Wed Oct 24 16:13:54 2012
Results reported at Wed Oct 24 16:14:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000069.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6348-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6348-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6348-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.50 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6348-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34530744
Writing coverage FWB file PRAD-G9-6348-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: PRAD-G9-6348-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6348-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 4402962: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000070> was used as the working directory.
Started at Wed Oct 24 16:14:20 2012
Results reported at Wed Oct 24 16:14:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000070.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6356-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6356-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6356-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.35 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6356-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000214.1
Ignoring chrom=GL000214.1
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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34345831
Writing coverage FWB file PRAD-G9-6356-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: PRAD-G9-6356-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6356-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 4402968: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000071> was used as the working directory.
Started at Wed Oct 24 16:14:20 2012
Results reported at Wed Oct 24 16:14:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000071.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6362-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6362-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6362-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     30.42 sec.
    Max Memory :      4729 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6362-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000214.1
Ignoring chrom=GL000214.1
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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
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=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 34309943
Writing coverage FWB file PRAD-G9-6362-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: PRAD-G9-6362-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6362-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 4402971: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000072> was used as the working directory.
Started at Wed Oct 24 16:14:34 2012
Results reported at Wed Oct 24 16:14:55 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000072.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6363-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6363-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6363-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.53 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6363-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=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=GL000237.1
Ignoring chrom=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34359504
Writing coverage FWB file PRAD-G9-6363-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: PRAD-G9-6363-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6363-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 4402975: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000073> was used as the working directory.
Started at Wed Oct 24 16:14:45 2012
Results reported at Wed Oct 24 16:15:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000073.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6364-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6364-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6364-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     15.75 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6364-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1

  Total coverage = 34472545
Writing coverage FWB file PRAD-G9-6364-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: PRAD-G9-6364-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6364-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 4402979: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000074> was used as the working directory.
Started at Wed Oct 24 16:14:57 2012
Results reported at Wed Oct 24 16:15:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000074.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6365-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6365-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6365-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.73 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6365-01.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=MT
Ignoring chrom=MT
Ignoring chrom=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=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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34416096
Writing coverage FWB file PRAD-G9-6365-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: PRAD-G9-6365-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6365-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4402984: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, 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/216151/iteration1/scatter.0000000075> was used as the working directory.
Started at Wed Oct 24 16:15:10 2012
Results reported at Wed Oct 24 16:15:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000075.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6367-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6367-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6367-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.21 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6367-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34889979
Writing coverage FWB file PRAD-G9-6367-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: PRAD-G9-6367-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6367-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1559>
Subject: Job 4402990: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1559>, 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/216151/iteration1/scatter.0000000076> was used as the working directory.
Started at Wed Oct 24 16:15:22 2012
Results reported at Wed Oct 24 16:15:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000076.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6370-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6370-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6370-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     32.09 sec.
    Max Memory :      4735 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6370-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=GL000209.1
Ignoring chrom=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34230662
Writing coverage FWB file PRAD-G9-6370-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: PRAD-G9-6370-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6370-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 4402995: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000077> was used as the working directory.
Started at Wed Oct 24 16:15:22 2012
Results reported at Wed Oct 24 16:15:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000077.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6371-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6371-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6371-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     29.36 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6371-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000214.1
Ignoring chrom=GL000214.1
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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34385390
Writing coverage FWB file PRAD-G9-6371-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: PRAD-G9-6371-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6371-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 4403000: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000078> was used as the working directory.
Started at Wed Oct 24 16:15:24 2012
Results reported at Wed Oct 24 16:15:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000078.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6373-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6373-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6373-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     17.97 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6373-01.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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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
Ignoring chrom=GL000192.1

  Total coverage = 34661887
Writing coverage FWB file PRAD-G9-6373-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: PRAD-G9-6373-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6373-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 4403004: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000079> was used as the working directory.
Started at Wed Oct 24 16:16:02 2012
Results reported at Wed Oct 24 16:16:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000079.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6378-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6378-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6378-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     29.61 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6378-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 35108710
Writing coverage FWB file PRAD-G9-6378-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: PRAD-G9-6378-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6378-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 4403010: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000080> was used as the working directory.
Started at Wed Oct 24 16:16:12 2012
Results reported at Wed Oct 24 16:16:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000080.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6384-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6384-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6384-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.12 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6384-01.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=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000214.1
Ignoring chrom=GL000214.1
Ignoring chrom=GL000214.1
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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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 = 34522603
Writing coverage FWB file PRAD-G9-6384-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: PRAD-G9-6384-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6384-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1559>
Subject: Job 4403013: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1559>, 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/216151/iteration1/scatter.0000000081> was used as the working directory.
Started at Wed Oct 24 16:16:23 2012
Results reported at Wed Oct 24 16:16:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000081.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6385-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6385-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6385-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     33.74 sec.
    Max Memory :      4734 MB
    Max Swap   :      5524 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6385-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=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=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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=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=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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000212.1
Ignoring chrom=GL000212.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34261616
Writing coverage FWB file PRAD-G9-6385-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: PRAD-G9-6385-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6385-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 4403019: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000082> was used as the working directory.
Started at Wed Oct 24 16:16:23 2012
Results reported at Wed Oct 24 16:16:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000082.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6494-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6494-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6494-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     19.40 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6494-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
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=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=GL000191.1
Ignoring chrom=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=GL000214.1
Ignoring chrom=GL000214.1
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=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=GL000218.1
Ignoring chrom=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=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=GL000213.1
Ignoring chrom=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=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=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=GL000223.1
Ignoring chrom=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=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
Ignoring chrom=GL000222.1
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=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
Ignoring chrom=GL000192.1
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 = 34222789
Writing coverage FWB file PRAD-G9-6494-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: PRAD-G9-6494-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6494-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 4403025: <scatter_216151> Done

Job <scatter_216151> was submitted from host <node1719> 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/216151/iteration1/scatter.0000000083> was used as the working directory.
Started at Wed Oct 24 16:16:35 2012
Results reported at Wed Oct 24 16:16:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/iteration1/scatter.0000000083.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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 "PRAD-G9-6496-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "PRAD-G9-6496-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6496-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216151/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   :     16.49 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/prad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_PRAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-G9-6496-01.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=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=MT
Ignoring chrom=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=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000241.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
Ignoring chrom=GL000237.1
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=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
Ignoring chrom=GL000228.1
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=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=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=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=GL000211.1
Ignoring chrom=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=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=GL000219.1
Ignoring chrom=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=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
Ignoring chrom=GL000195.1
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=GL000194.1
Ignoring chrom=GL000194.1
Ignoring chrom=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

  Total coverage = 34271961
Writing coverage FWB file PRAD-G9-6496-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: PRAD-G9-6496-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: PRAD-G9-6496-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


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.

