calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/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.50.3134/prepare.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68683/STAD.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68683/STAD.patients.txt /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68683/STAD.maf
Started submitting scatter jobs at Thu Mar 29 05:44:23 2012
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/68684/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000001/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-B7-5816" "STAD-B7-5816.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-B7-5816-01.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/68684/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000002/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-B7-5818" "STAD-B7-5818.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-B7-5818-01.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/68684/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000003/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4183" "STAD-BR-4183.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4183-01.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/68684/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000004/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4184" "STAD-BR-4184.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4184-01.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/68684/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000005/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4187" "STAD-BR-4187.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4187-01.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/68684/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000006/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4188" "STAD-BR-4188.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4188-01.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/68684/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000007/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4190" "STAD-BR-4190.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4190-01.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/68684/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000008/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4191" "STAD-BR-4191.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4191-01.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/68684/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000009/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4194" "STAD-BR-4194.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4194-01.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/68684/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000010/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4195" "STAD-BR-4195.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4195-01.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/68684/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000011/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4199" "STAD-BR-4199.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4199-01.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/68684/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000012/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4200" "STAD-BR-4200.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4200-01.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/68684/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000013/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4201" "STAD-BR-4201.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4201-01.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/68684/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000014/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4253" "STAD-BR-4253.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4253-01.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/68684/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000015/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4255" "STAD-BR-4255.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4255-01.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/68684/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000016/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4256" "STAD-BR-4256.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4256-01.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/68684/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000017/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4257" "STAD-BR-4257.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4257-01.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/68684/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000018/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4259" "STAD-BR-4259.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4259-01.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/68684/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000019/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4261" "STAD-BR-4261.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4261-01.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/68684/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000020/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4265" "STAD-BR-4265.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4265-01.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/68684/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000021/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4267" "STAD-BR-4267.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4267-01.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/68684/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000022/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4277" "STAD-BR-4277.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4277-01.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/68684/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000023/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4278" "STAD-BR-4278.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4278-01.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/68684/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000024/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4279" "STAD-BR-4279.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4279-01.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/68684/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000025/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4280" "STAD-BR-4280.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4280-01.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/68684/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000026/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4281" "STAD-BR-4281.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4281-01.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/68684/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000027/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4284" "STAD-BR-4284.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4284-01.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/68684/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000028/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4288" "STAD-BR-4288.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4288-01.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/68684/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000029/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4291" "STAD-BR-4291.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4291-01.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/68684/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000030/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4292" "STAD-BR-4292.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4292-01.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/68684/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000031/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4294" "STAD-BR-4294.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4294-01.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/68684/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000032/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4298" "STAD-BR-4298.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4298-01.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/68684/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000033/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4357" "STAD-BR-4357.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4357-01.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/68684/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000034/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4361" "STAD-BR-4361.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4361-01.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/68684/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000035/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4362" "STAD-BR-4362.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4362-01.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/68684/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000036/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4363" "STAD-BR-4363.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4363-01.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/68684/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000037/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4366" "STAD-BR-4366.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4366-01.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/68684/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000038/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4367" "STAD-BR-4367.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4367-01.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/68684/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000039/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4368" "STAD-BR-4368.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4368-01.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/68684/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000040/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4369" "STAD-BR-4369.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4369-01.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/68684/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000041/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4370" "STAD-BR-4370.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4370-01.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/68684/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000042/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4371" "STAD-BR-4371.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4371-01.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/68684/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000043/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4375" "STAD-BR-4375.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4375-01.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/68684/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000044/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-4376" "STAD-BR-4376.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-4376-01.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/68684/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000045/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6452" "STAD-BR-6452.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6452-01.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/68684/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000046/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6453" "STAD-BR-6453.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6453-01.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/68684/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000047/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6454" "STAD-BR-6454.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6454-01.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/68684/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000048/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6455" "STAD-BR-6455.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6455-01.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/68684/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000049/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6456" "STAD-BR-6456.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6456-01.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/68684/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000050/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6457" "STAD-BR-6457.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6457-01.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/68684/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000051/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6458" "STAD-BR-6458.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6458-01.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/68684/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000052/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6564" "STAD-BR-6564.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6564-01.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/68684/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000053/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6565" "STAD-BR-6565.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6565-01.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/68684/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000054/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6566" "STAD-BR-6566.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6566-01.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/68684/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000055/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6705" "STAD-BR-6705.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6705-01.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/68684/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000056/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6706" "STAD-BR-6706.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6706-01.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/68684/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000057/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6707" "STAD-BR-6707.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6707-01.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/68684/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000058/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6709" "STAD-BR-6709.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6709-01.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/68684/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000059/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6710" "STAD-BR-6710.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6710-01.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/68684/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000060/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6801" "STAD-BR-6801.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6801-01.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/68684/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000061/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6802" "STAD-BR-6802.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6802-01.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/68684/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000062/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6803" "STAD-BR-6803.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6803-01.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/68684/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000063/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-BR-6852" "STAD-BR-6852.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-BR-6852-01.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/68684/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000064/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CD-5798" "STAD-CD-5798.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CD-5798-01.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/68684/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000065/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CD-5799" "STAD-CD-5799.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CD-5799-01.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/68684/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000066/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CD-5800" "STAD-CD-5800.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CD-5800-01.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/68684/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000067/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CD-5801" "STAD-CD-5801.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CD-5801-01.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/68684/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000068/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CD-5802" "STAD-CD-5802.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CD-5802-01.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/68684/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000069/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CD-5803" "STAD-CD-5803.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CD-5803-01.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/68684/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000070/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CD-5813" "STAD-CD-5813.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CD-5813-01.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/68684/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000071/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4300" "STAD-CG-4300.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4300-01.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/68684/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000072/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4301" "STAD-CG-4301.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4301-01.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/68684/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000073/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4304" "STAD-CG-4304.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4304-01.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/68684/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000074/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4305" "STAD-CG-4305.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4305-01.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/68684/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000075/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4306" "STAD-CG-4306.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4306-01.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/68684/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000076/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4436" "STAD-CG-4436.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4436-01.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/68684/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000077/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4437" "STAD-CG-4437.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4437-01.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/68684/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000078/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4438" "STAD-CG-4438.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4438-01.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/68684/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000079/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4440" "STAD-CG-4440.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4440-01.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/68684/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000080/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4441" "STAD-CG-4441.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4441-01.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/68684/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000081/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4442" "STAD-CG-4442.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4442-01.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/68684/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000082/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4443" "STAD-CG-4443.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4443-01.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/68684/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000083/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4444" "STAD-CG-4444.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4444-01.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/68684/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000084/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4449" "STAD-CG-4449.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4449-01.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/68684/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000085/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4455" "STAD-CG-4455.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4455-01.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/68684/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000086/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4460" "STAD-CG-4460.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4460-01.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/68684/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000087/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4462" "STAD-CG-4462.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4462-01.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/68684/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000088/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4465" "STAD-CG-4465.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4465-01.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/68684/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000089/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4466" "STAD-CG-4466.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4466-01.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/68684/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000090/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4469" "STAD-CG-4469.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4469-01.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/68684/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000091/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4472" "STAD-CG-4472.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4472-01.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/68684/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000092/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4474" "STAD-CG-4474.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4474-01.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/68684/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000093/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4475" "STAD-CG-4475.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4475-01.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/68684/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000094/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4476" "STAD-CG-4476.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4476-01.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/68684/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000095/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-4477" "STAD-CG-4477.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-4477-01.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/68684/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000096/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5716" "STAD-CG-5716.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5716-01.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/68684/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000097/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5717" "STAD-CG-5717.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5717-01.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/68684/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000098/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5718" "STAD-CG-5718.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5718-01.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/68684/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000099/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5719" "STAD-CG-5719.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5719-01.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/68684/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000100/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5720" "STAD-CG-5720.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5720-01.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/68684/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000101/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5721" "STAD-CG-5721.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5721-01.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/68684/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000102/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5722" "STAD-CG-5722.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5722-01.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/68684/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000103/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5723" "STAD-CG-5723.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5723-01.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/68684/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000104/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5724" "STAD-CG-5724.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5724-01.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/68684/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000105/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5725" "STAD-CG-5725.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5725-01.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/68684/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000106/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5726" "STAD-CG-5726.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5726-01.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/68684/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000107/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5727" "STAD-CG-5727.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5727-01.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/68684/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000108/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5728" "STAD-CG-5728.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5728-01.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/68684/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000109/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5730" "STAD-CG-5730.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5730-01.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/68684/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000110/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5732" "STAD-CG-5732.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5732-01.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/68684/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000111/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5733" "STAD-CG-5733.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5733-01.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/68684/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000112/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-CG-5734" "STAD-CG-5734.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-CG-5734-01.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/68684/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000113/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-5577" "STAD-D7-5577.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-5577-01.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/68684/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000114/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-5578" "STAD-D7-5578.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-5578-01.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/68684/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000115/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-5579" "STAD-D7-5579.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-5579-01.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/68684/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000116/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6518" "STAD-D7-6518.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6518-01.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/68684/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000117/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6519" "STAD-D7-6519.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6519-01.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/68684/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000118/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6520" "STAD-D7-6520.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6520-01.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/68684/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000119/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6521" "STAD-D7-6521.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6521-01.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/68684/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000120/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6522" "STAD-D7-6522.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6522-01.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/68684/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000121/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6524" "STAD-D7-6524.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6524-01.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/68684/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000122/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6525" "STAD-D7-6525.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6525-01.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/68684/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000123/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6526" "STAD-D7-6526.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6526-01.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/68684/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000124/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6527" "STAD-D7-6527.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6527-01.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/68684/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000125/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6528" "STAD-D7-6528.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6528-01.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/68684/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000126/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6815" "STAD-D7-6815.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6815-01.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/68684/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000127/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6817" "STAD-D7-6817.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6817-01.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/68684/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000128/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6818" "STAD-D7-6818.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6818-01.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/68684/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000129/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6820" "STAD-D7-6820.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6820-01.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/68684/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000130/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-D7-6822" "STAD-D7-6822.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-D7-6822-01.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/68684/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000131/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-EQ-5647" "STAD-EQ-5647.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-EQ-5647-01.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/68684/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000132/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-F1-6177" "STAD-F1-6177.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-F1-6177-01.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/68684/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68684/iteration1/scatter.0000000133/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_68684   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "STAD-F1-6874" "STAD-F1-6874.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/stad/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_STAD.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-F1-6874-01.wig.txt"

Finished submitting scatter jobs at Thu Mar 29 05:46:06 2012 in 1.70856571595 minutes
calling:  bsub -E cd "/xchip/cga1" && 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_68684) -J gather_68684 -P Firehose -R rusage[mem=7] -sp 65   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/run_matlab.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ fh_MutSigCoverageGather   "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/" "STAD" "/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68683/STAD.maf" "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65" "4" "/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/68683/STAD.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_68684) -J iteration_68684 -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 68684 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/
Path iteration1 exists:  True
