calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1 -E cd "/xchip/tcga" && cd "/xchip/cga" -e prepare.err -oo prepare.out -K -P Firehose python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/prepare.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC-TP/2283691/0.MutSigPreprocess.Finished/CESC-TP.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC-TP/2283691/0.MutSigPreprocess.Finished/CESC-TP.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC-TP/2283691/0.MutSigPreprocess.Finished/CESC-TP.maf
Started submitting scatter jobs at Thu Jan 10 14:04:00 2013
calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000001/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-BI-A0VR-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000002/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-BI-A0VS-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000003/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A0TN-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000004/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BE-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000005/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BF-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000006/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BI-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000007/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BJ-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000008/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BK-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000009/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BL-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000010/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BM-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000011/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1BN-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000012/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M5-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000013/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M6-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000014/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M7-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000015/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M8-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000016/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1M9-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000017/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1ME-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000018/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MF-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000019/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MH-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000020/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MI-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000021/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MJ-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000022/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MK-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000023/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1ML-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000024/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MN-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000025/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MP-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000026/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-C5-A1MQ-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000027/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DR-A0ZL-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000028/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DR-A0ZM-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000029/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DS-A0VK-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000030/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DS-A0VL-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000031/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DS-A0VM-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000032/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-DS-A0VN-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000033/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-EA-A1QT-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000034/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-EX-A1H5-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000035/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-FU-A23K-TP.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"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285806/iteration1/scatter.0000000036/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_285806   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/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-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "CESC-FU-A23L-TP.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"

Finished submitting scatter jobs at Thu Jan 10 14:05:27 2013 in 1.45182063182 minutes
calling:  bsub -E cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -q cga -R select[tmp>1000 && scratch>1] -e scatter-gather.err.txt -o scatter-gather.out.txt -w ended(scatter_285806) -J gather_285806 -P Firehose -R rusage[mem=12] -sp 65   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-TP" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC-TP/2283691/0.MutSigPreprocess.Finished/CESC-TP.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-TP/2283691/0.MutSigPreprocess.Finished/CESC-TP.patients.txt"

calling:  bsub -E cd "/xchip/cga" -q cga -R select[tmp>1000 && scratch>1] -e iterator.err.txt -o iterator.out.txt -w ended(gather_285806) -J iteration_285806 -P Firehose -sp 65   /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 285806 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
Path iteration1 exists:  True
