Sender: LSF System <lsf@node1427>
Subject: Job 4434565: <iteration_161827> Done

Job <iteration_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1427>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827> was used as the working directory.
Started at Tue Sep  4 08:09:52 2012
Results reported at Tue Sep  4 08:09:58 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 ${return_code} > exited;
exit 1;
fi
/xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 161827 --priority 50 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
return_code=$?
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/161827
rmdir iteration*
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :      0.99 sec.
    Max Memory :         5 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

starting
ls: iteration*/exited: No such file or directory
ls: exited: No such file or directory
Running scatter-gather-iterator with the following args: /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 161827 --priority 50 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@node1706>
Subject: Job 4434563: <gather_161827> Done

Job <gather_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1706>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1> was used as the working directory.
Started at Tue Sep  4 07:56:13 2012
Results reported at Tue Sep  4 08:09:51 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 36 ]; 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/" "CESC" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1685861/0.MutSigPreprocess.Finished/CESC.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/CESC/1685861/0.MutSigPreprocess.Finished/CESC.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   :    683.42 sec.
    Max Memory :      5053 MB
    Max Swap   :      6729 MB

    Max Processes  :         6
    Max Threads    :        52

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
36 files found
36 files found
36 files found
Creating summed FWB coverage file: ./CESC.summed_coverage.fwb
Loading target file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Opening files: 10/36 20/36 30/36 
Summing and writing output file:
1/4283949 Elapsed time is 0.007045 seconds.
100001/4283949 Elapsed time is 0.761927 seconds.
200001/4283949 Elapsed time is 1.224336 seconds.
300001/4283949 Elapsed time is 1.299901 seconds.
400001/4283949 Elapsed time is 1.366698 seconds.
500001/4283949 Elapsed time is 1.439088 seconds.
600001/4283949 Elapsed time is 1.559901 seconds.
700001/4283949 Elapsed time is 1.685902 seconds.
800001/4283949 Elapsed time is 1.802867 seconds.
900001/4283949 Elapsed time is 1.913265 seconds.
1000001/4283949 Elapsed time is 2.030241 seconds.
1100001/4283949 Elapsed time is 2.120691 seconds.
1200001/4283949 Elapsed time is 2.187953 seconds.
1300001/4283949 Elapsed time is 2.256038 seconds.
1400001/4283949 Elapsed time is 2.323545 seconds.
1500001/4283949 Elapsed time is 2.390603 seconds.
1600001/4283949 Elapsed time is 2.458167 seconds.
1700001/4283949 Elapsed time is 2.525914 seconds.
1800001/4283949 Elapsed time is 2.595092 seconds.
1900001/4283949 Elapsed time is 2.662253 seconds.
2000001/4283949 Elapsed time is 2.731091 seconds.
2100001/4283949 Elapsed time is 2.892361 seconds.
2200001/4283949 Elapsed time is 2.961669 seconds.
2300001/4283949 Elapsed time is 3.031748 seconds.
2400001/4283949 Elapsed time is 3.100037 seconds.
2500001/4283949 Elapsed time is 3.168609 seconds.
2600001/4283949 Elapsed time is 3.235846 seconds.
2700001/4283949 Elapsed time is 3.303587 seconds.
2800001/4283949 Elapsed time is 3.371355 seconds.
2900001/4283949 Elapsed time is 3.438674 seconds.
3000001/4283949 Elapsed time is 3.558434 seconds.
3100001/4283949 Elapsed time is 3.685998 seconds.
3200001/4283949 Elapsed time is 3.816497 seconds.
3300001/4283949 Elapsed time is 3.944970 seconds.
3400001/4283949 Elapsed time is 4.015272 seconds.
3500001/4283949 Elapsed time is 4.084164 seconds.
3600001/4283949 Elapsed time is 4.153449 seconds.
3700001/4283949 Elapsed time is 4.223575 seconds.
3800001/4283949 Elapsed time is 4.293345 seconds.
3900001/4283949 Elapsed time is 4.361809 seconds.
4000001/4283949 Elapsed time is 4.429860 seconds.
4100001/4283949 Elapsed time is 4.499161 seconds.
4200001/4283949 Elapsed time is 4.567319 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  7201 N 3143245254  rate 2.29e-06 (1.00x)  ci 2.24e-06 to 2.34e-06

k=2
                Tp*N->mut   n  5294 N  639469560  rate 8.28e-06 (3.61x)  ci 8.06e-06 to 8.50e-06
          (A/C/G)p*N->mut   n  1907 N 2503775694  rate 7.62e-07 (0.33x)  ci 7.28e-07 to 7.97e-07

k=3
                Tp*C->mut   n  5218 N  417711420  rate 1.25e-05 (5.45x)  ci 1.22e-05 to 1.28e-05
          (A/C/G)p*C->mut   n  1572 N 1179370200  rate 1.33e-06 (0.58x)  ci 1.27e-06 to 1.40e-06
                   A->mut   n   411 N 1546163634  rate 2.66e-07 (0.12x)  ci 2.41e-07 to 2.93e-07

k=4
              Tp*C->(T/G)   n  4889 N  278474280  rate 1.76e-05 (7.66x)  ci 1.71e-05 to 1.81e-05
                  Tp*C->A   n   329 N  139237140  rate 2.36e-06 (1.03x)  ci 2.11e-06 to 2.63e-06
          (A/C/G)p*C->mut   n  1572 N 1179370200  rate 1.33e-06 (0.58x)  ci 1.27e-06 to 1.40e-06
                   A->mut   n   411 N 1546163634  rate 2.66e-07 (0.12x)  ci 2.41e-07 to 2.93e-07

Saving ./CESC.mutcategs.txt
all files are *.bin: will read in BINARY MODE
36 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 107296906: appears to include noncoding areas
1/36 Loading ./CESC.covfiles/CESC-BI-A0VR.somatic_coverage.txt.bin
2/36 Loading ./CESC.covfiles/CESC-BI-A0VS.somatic_coverage.txt.bin
3/36 Loading ./CESC.covfiles/CESC-C5-A0TN.somatic_coverage.txt.bin
4/36 Loading ./CESC.covfiles/CESC-C5-A1BE.somatic_coverage.txt.bin
5/36 Loading ./CESC.covfiles/CESC-C5-A1BF.somatic_coverage.txt.bin
6/36 Loading ./CESC.covfiles/CESC-C5-A1BI.somatic_coverage.txt.bin
7/36 Loading ./CESC.covfiles/CESC-C5-A1BJ.somatic_coverage.txt.bin
8/36 Loading ./CESC.covfiles/CESC-C5-A1BK.somatic_coverage.txt.bin
9/36 Loading ./CESC.covfiles/CESC-C5-A1BL.somatic_coverage.txt.bin
10/36 Loading ./CESC.covfiles/CESC-C5-A1BM.somatic_coverage.txt.bin
11/36 Loading ./CESC.covfiles/CESC-C5-A1BN.somatic_coverage.txt.bin
12/36 Loading ./CESC.covfiles/CESC-C5-A1M5.somatic_coverage.txt.bin
13/36 Loading ./CESC.covfiles/CESC-C5-A1M6.somatic_coverage.txt.bin
14/36 Loading ./CESC.covfiles/CESC-C5-A1M7.somatic_coverage.txt.bin
15/36 Loading ./CESC.covfiles/CESC-C5-A1M8.somatic_coverage.txt.bin
16/36 Loading ./CESC.covfiles/CESC-C5-A1M9.somatic_coverage.txt.bin
17/36 Loading ./CESC.covfiles/CESC-C5-A1ME.somatic_coverage.txt.bin
18/36 Loading ./CESC.covfiles/CESC-C5-A1MF.somatic_coverage.txt.bin
19/36 Loading ./CESC.covfiles/CESC-C5-A1MH.somatic_coverage.txt.bin
20/36 Loading ./CESC.covfiles/CESC-C5-A1MI.somatic_coverage.txt.bin
21/36 Loading ./CESC.covfiles/CESC-C5-A1MJ.somatic_coverage.txt.bin
22/36 Loading ./CESC.covfiles/CESC-C5-A1MK.somatic_coverage.txt.bin
23/36 Loading ./CESC.covfiles/CESC-C5-A1ML.somatic_coverage.txt.bin
24/36 Loading ./CESC.covfiles/CESC-C5-A1MN.somatic_coverage.txt.bin
25/36 Loading ./CESC.covfiles/CESC-C5-A1MP.somatic_coverage.txt.bin
26/36 Loading ./CESC.covfiles/CESC-C5-A1MQ.somatic_coverage.txt.bin
27/36 Loading ./CESC.covfiles/CESC-DR-A0ZL.somatic_coverage.txt.bin
28/36 Loading ./CESC.covfiles/CESC-DR-A0ZM.somatic_coverage.txt.bin
29/36 Loading ./CESC.covfiles/CESC-DS-A0VK.somatic_coverage.txt.bin
30/36 Loading ./CESC.covfiles/CESC-DS-A0VL.somatic_coverage.txt.bin
31/36 Loading ./CESC.covfiles/CESC-DS-A0VM.somatic_coverage.txt.bin
32/36 Loading ./CESC.covfiles/CESC-DS-A0VN.somatic_coverage.txt.bin
33/36 Loading ./CESC.covfiles/CESC-EA-A1QT.somatic_coverage.txt.bin
34/36 Loading ./CESC.covfiles/CESC-EX-A1H5.somatic_coverage.txt.bin
35/36 Loading ./CESC.covfiles/CESC-FU-A23K.somatic_coverage.txt.bin
36/36 Loading ./CESC.covfiles/CESC-FU-A23L.somatic_coverage.txt.bin
Saving ./CESC.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/161827/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/ CESC /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1685861/0.MutSigPreprocess.Finished/CESC.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/CESC/1685861/0.MutSigPreprocess.Finished/CESC.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@node1714>
Subject: Job 4434515: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1714>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000001> was used as the working directory.
Started at Tue Sep  4 07:26:33 2012
Results reported at Tue Sep  4 07:27:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000001.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-BI-A0VR" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-BI-A0VR.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-BI-A0VR-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.69 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-BI-A0VR-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33714787
Writing coverage FWB file CESC-BI-A0VR.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-BI-A0VR.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-BI-A0VR.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434517: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000002> was used as the working directory.
Started at Tue Sep  4 07:26:33 2012
Results reported at Tue Sep  4 07:26:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000002.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-BI-A0VS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-BI-A0VS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-BI-A0VS-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.92 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-BI-A0VS-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33653587
Writing coverage FWB file CESC-BI-A0VS.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-BI-A0VS.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-BI-A0VS.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1703>
Subject: Job 4434518: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1703>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000003> was used as the working directory.
Started at Tue Sep  4 07:27:15 2012
Results reported at Tue Sep  4 07:27:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000003.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A0TN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A0TN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A0TN-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.76 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A0TN-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32446793
Writing coverage FWB file CESC-C5-A0TN.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A0TN.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A0TN.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1648>
Subject: Job 4434519: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000004> was used as the working directory.
Started at Tue Sep  4 07:27:32 2012
Results reported at Tue Sep  4 07:27:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000004.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1BE" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BE.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BE-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.26 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BE-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32784353
Writing coverage FWB file CESC-C5-A1BE.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1BE.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1BE.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434520: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000005> was used as the working directory.
Started at Tue Sep  4 07:27:32 2012
Results reported at Tue Sep  4 07:27:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000005.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1BF" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BF.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BF-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.25 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BF-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32797681
Writing coverage FWB file CESC-C5-A1BF.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1BF.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1BF.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1648>
Subject: Job 4434521: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000006> was used as the working directory.
Started at Tue Sep  4 07:28:37 2012
Results reported at Tue Sep  4 07:29:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000006.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1BI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BI-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     17.54 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BI-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32713306
Writing coverage FWB file CESC-C5-A1BI.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1BI.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1BI.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434523: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000007> was used as the working directory.
Started at Tue Sep  4 07:28:37 2012
Results reported at Tue Sep  4 07:29:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000007.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1BJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BJ-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.15 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BJ-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32616047
Writing coverage FWB file CESC-C5-A1BJ.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1BJ.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1BJ.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1703>
Subject: Job 4434525: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1703>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000008> was used as the working directory.
Started at Tue Sep  4 07:29:20 2012
Results reported at Tue Sep  4 07:29:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000008.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1BK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BK-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.15 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BK-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32802972
Writing coverage FWB file CESC-C5-A1BK.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1BK.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1BK.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1714>
Subject: Job 4434526: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1714>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000009> was used as the working directory.
Started at Tue Sep  4 07:29:29 2012
Results reported at Tue Sep  4 07:29:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000009.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1BL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BL-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.11 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BL-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32719735
Writing coverage FWB file CESC-C5-A1BL.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1BL.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1BL.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1648>
Subject: Job 4434527: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000010> was used as the working directory.
Started at Tue Sep  4 07:29:38 2012
Results reported at Tue Sep  4 07:30:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000010.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1BM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BM-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.47 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BM-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32631360
Writing coverage FWB file CESC-C5-A1BM.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1BM.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1BM.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1703>
Subject: Job 4434528: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1703>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000011> was used as the working directory.
Started at Tue Sep  4 07:30:19 2012
Results reported at Tue Sep  4 07:30:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000011.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1BN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BN-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.05 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1BN-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 31944499
Writing coverage FWB file CESC-C5-A1BN.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1BN.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1BN.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1714>
Subject: Job 4434530: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1714>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000012> was used as the working directory.
Started at Tue Sep  4 07:30:31 2012
Results reported at Tue Sep  4 07:30:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000012.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1M5" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M5.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M5-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.29 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M5-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32468867
Writing coverage FWB file CESC-C5-A1M5.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1M5.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1M5.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1703>
Subject: Job 4434531: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1703>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000013> was used as the working directory.
Started at Tue Sep  4 07:31:19 2012
Results reported at Tue Sep  4 07:31:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000013.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1M6" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M6.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M6-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.56 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M6-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32623049
Writing coverage FWB file CESC-C5-A1M6.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1M6.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1M6.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1648>
Subject: Job 4434533: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000014> was used as the working directory.
Started at Tue Sep  4 07:31:42 2012
Results reported at Tue Sep  4 07:32:02 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000014.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1M7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M7-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000014.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.97 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M7-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32602187
Writing coverage FWB file CESC-C5-A1M7.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1M7.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1M7.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1649>
Subject: Job 4434534: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000015> was used as the working directory.
Started at Tue Sep  4 07:31:54 2012
Results reported at Tue Sep  4 07:32:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000015.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1M8" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M8.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M8-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.14 sec.
    Max Memory :         4 MB
    Max Swap   :        46 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M8-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32327799
Writing coverage FWB file CESC-C5-A1M8.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1M8.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1M8.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434535: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000016> was used as the working directory.
Started at Tue Sep  4 07:32:23 2012
Results reported at Tue Sep  4 07:32:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000016.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1M9" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M9.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M9-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.56 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1M9-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32799778
Writing coverage FWB file CESC-C5-A1M9.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1M9.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1M9.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1648>
Subject: Job 4434536: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000017> was used as the working directory.
Started at Tue Sep  4 07:33:43 2012
Results reported at Tue Sep  4 07:34:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000017.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1ME" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1ME.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1ME-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.52 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1ME-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32194566
Writing coverage FWB file CESC-C5-A1ME.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1ME.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1ME.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1700>
Subject: Job 4434538: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000018> was used as the working directory.
Started at Tue Sep  4 07:33:43 2012
Results reported at Tue Sep  4 07:37:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000018.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1MF" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MF.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MF-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     18.59 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MF-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32153424
Writing coverage FWB file CESC-C5-A1MF.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1MF.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1MF.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1648>
Subject: Job 4434539: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000019> was used as the working directory.
Started at Tue Sep  4 07:34:45 2012
Results reported at Tue Sep  4 07:35:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000019.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1MH" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MH.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MH-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     17.64 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MH-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32103014
Writing coverage FWB file CESC-C5-A1MH.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1MH.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1MH.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434541: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000020> was used as the working directory.
Started at Tue Sep  4 07:35:24 2012
Results reported at Tue Sep  4 07:35:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000020.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1MI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MI-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.99 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MI-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32290143
Writing coverage FWB file CESC-C5-A1MI.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1MI.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1MI.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1649>
Subject: Job 4434542: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000021> was used as the working directory.
Started at Tue Sep  4 07:35:55 2012
Results reported at Tue Sep  4 07:36:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000021.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1MJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MJ-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     17.39 sec.
    Max Memory :         4 MB
    Max Swap   :        46 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MJ-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32164884
Writing coverage FWB file CESC-C5-A1MJ.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1MJ.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1MJ.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434543: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000022> was used as the working directory.
Started at Tue Sep  4 07:36:23 2012
Results reported at Tue Sep  4 07:36:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000022.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1MK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MK-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.73 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MK-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32429338
Writing coverage FWB file CESC-C5-A1MK.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1MK.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1MK.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1649>
Subject: Job 4434544: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000023> was used as the working directory.
Started at Tue Sep  4 07:36:55 2012
Results reported at Tue Sep  4 07:37:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000023.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1ML" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1ML.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1ML-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.71 sec.
    Max Memory :         4 MB
    Max Swap   :        46 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1ML-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 31859915
Writing coverage FWB file CESC-C5-A1ML.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1ML.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1ML.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434545: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000024> was used as the working directory.
Started at Tue Sep  4 07:37:24 2012
Results reported at Tue Sep  4 07:37:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000024.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1MN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MN-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.02 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MN-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32135208
Writing coverage FWB file CESC-C5-A1MN.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1MN.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1MN.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1649>
Subject: Job 4434547: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000025> was used as the working directory.
Started at Tue Sep  4 07:37:56 2012
Results reported at Tue Sep  4 07:38:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000025.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1MP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MP-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.47 sec.
    Max Memory :         4 MB
    Max Swap   :        46 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MP-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32244880
Writing coverage FWB file CESC-C5-A1MP.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1MP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1MP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1710>
Subject: Job 4434548: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000026> was used as the working directory.
Started at Tue Sep  4 07:37:59 2012
Results reported at Tue Sep  4 07:46:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000026.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-C5-A1MQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MQ-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     22.96 sec.
    Max Memory :      4738 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-C5-A1MQ-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32320295
Writing coverage FWB file CESC-C5-A1MQ.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-C5-A1MQ.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-C5-A1MQ.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434550: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000027> was used as the working directory.
Started at Tue Sep  4 07:38:27 2012
Results reported at Tue Sep  4 07:38:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000027.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-DR-A0ZL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DR-A0ZL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DR-A0ZL-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.85 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DR-A0ZL-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33838173
Writing coverage FWB file CESC-DR-A0ZL.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-DR-A0ZL.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-DR-A0ZL.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1700>
Subject: Job 4434551: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000028> was used as the working directory.
Started at Tue Sep  4 07:38:32 2012
Results reported at Tue Sep  4 07:38:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000028.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-DR-A0ZM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DR-A0ZM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DR-A0ZM-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.25 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DR-A0ZM-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33751235
Writing coverage FWB file CESC-DR-A0ZM.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-DR-A0ZM.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-DR-A0ZM.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1709>
Subject: Job 4434553: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000029> was used as the working directory.
Started at Tue Sep  4 07:38:48 2012
Results reported at Tue Sep  4 07:42:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000029.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-DS-A0VK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DS-A0VK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VK-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     18.28 sec.
    Max Memory :      4738 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VK-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33761665
Writing coverage FWB file CESC-DS-A0VK.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-DS-A0VK.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-DS-A0VK.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1648>
Subject: Job 4434554: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000030> was used as the working directory.
Started at Tue Sep  4 07:38:48 2012
Results reported at Tue Sep  4 07:39:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000030.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-DS-A0VL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DS-A0VL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VL-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.98 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VL-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33123372
Writing coverage FWB file CESC-DS-A0VL.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-DS-A0VL.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-DS-A0VL.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1649>
Subject: Job 4434555: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000031> was used as the working directory.
Started at Tue Sep  4 07:39:00 2012
Results reported at Tue Sep  4 07:39:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000031.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-DS-A0VM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DS-A0VM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VM-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.03 sec.
    Max Memory :         4 MB
    Max Swap   :        46 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VM-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33672263
Writing coverage FWB file CESC-DS-A0VM.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-DS-A0VM.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-DS-A0VM.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1700>
Subject: Job 4434557: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000032> was used as the working directory.
Started at Tue Sep  4 07:39:36 2012
Results reported at Tue Sep  4 07:39:55 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000032.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-DS-A0VN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DS-A0VN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VN-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.75 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-DS-A0VN-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33740834
Writing coverage FWB file CESC-DS-A0VN.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-DS-A0VN.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-DS-A0VN.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1648>
Subject: Job 4434558: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000033> was used as the working directory.
Started at Tue Sep  4 07:39:51 2012
Results reported at Tue Sep  4 07:40:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000033.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-EA-A1QT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-EA-A1QT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-EA-A1QT-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.21 sec.
    Max Memory :         4 MB
    Max Swap   :        41 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-EA-A1QT-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32152698
Writing coverage FWB file CESC-EA-A1QT.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-EA-A1QT.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-EA-A1QT.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1649>
Subject: Job 4434559: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000034> was used as the working directory.
Started at Tue Sep  4 07:40:04 2012
Results reported at Tue Sep  4 07:40:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000034.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-EX-A1H5" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-EX-A1H5.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-EX-A1H5-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     16.02 sec.
    Max Memory :         4 MB
    Max Swap   :        47 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-EX-A1H5-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32671029
Writing coverage FWB file CESC-EX-A1H5.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-EX-A1H5.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-EX-A1H5.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1700>
Subject: Job 4434561: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> 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/161827/iteration1/scatter.0000000035> was used as the working directory.
Started at Tue Sep  4 07:40:37 2012
Results reported at Tue Sep  4 07:40:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000035.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-FU-A23K" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-FU-A23K.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-FU-A23K-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.63 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-FU-A23K-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 33052991
Writing coverage FWB file CESC-FU-A23K.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-FU-A23K.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-FU-A23K.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1699>
Subject: Job 4434562: <scatter_161827> Done

Job <scatter_161827> was submitted from host <node464> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000036> was used as the working directory.
Started at Tue Sep  4 07:41:33 2012
Results reported at Tue Sep  4 07:41:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/iteration1/scatter.0000000036.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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 "CESC-FU-A23L" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-FU-A23L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-FU-A23L-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/161827/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   :     15.36 sec.
    Max Memory :         4 MB
    Max Swap   :        42 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/cesc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_CESC.IlluminaGA_DNASeq.Level_2.2.3.0/TCGA-FU-A23L-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 32691700
Writing coverage FWB file CESC-FU-A23L.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
Reading coverage file: CESC-FU-A23L.somatic_coverage.fwb
Reading categories file: /xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb
Writing binary output file: CESC-FU-A23L.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


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.

