calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1 -E cd "/xchip/tcga" && cd "/xchip/cga" -e prepare.err -oo prepare.out -K -P Firehose python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/prepare.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/0.MutSigPreprocess.Finished/LUSC.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/0.MutSigPreprocess.Finished/LUSC.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/0.MutSigPreprocess.Finished/LUSC.maf
Started submitting scatter jobs at Wed Oct 24 15:03:51 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/215414/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000001/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3406-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3406-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3406-01.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/215414/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000002/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3407-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3407-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3407-01.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/215414/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000003/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3408-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3408-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3408-01.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/215414/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000004/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3409-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3409-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3409-01.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/215414/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000005/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3410-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3410-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3410-01.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/215414/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000006/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3411-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3411-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3411-01.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/215414/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000007/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3412-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3412-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3412-01.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/215414/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000008/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3414-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3414-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3414-01.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/215414/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000009/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3415-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3415-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3415-01.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/215414/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000010/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3416-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3416-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3416-01.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/215414/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000011/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3417-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3417-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3417-01.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/215414/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000012/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3419-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3419-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3419-01.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/215414/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000013/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-3421-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-3421-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-3421-01.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/215414/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000014/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-4083-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-4083-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-4083-01.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/215414/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000015/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-4086-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-4086-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-4086-01.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/215414/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000016/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-4721-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-4721-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-4721-01.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/215414/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000017/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-5592-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-5592-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-5592-01.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/215414/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000018/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-18-5595-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-18-5595-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-18-5595-01.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/215414/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000019/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-1070-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-1070-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1070-01.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/215414/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000020/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-1071-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-1071-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1071-01.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/215414/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000021/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-1076-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-1076-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1076-01.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/215414/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000022/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-1077-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-1077-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1077-01.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/215414/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000023/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-1078-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-1078-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1078-01.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/215414/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000024/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-1081-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-1081-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-1081-01.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/215414/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000025/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-5782-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-5782-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-5782-01.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/215414/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000026/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-5784-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-5784-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-5784-01.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/215414/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000027/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-5786-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-5786-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-5786-01.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/215414/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000028/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-21-5787-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-21-5787-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-21-5787-01.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/215414/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000029/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-0944-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-0944-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-0944-01.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/215414/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000030/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-1002-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-1002-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-1002-01.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/215414/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000031/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-1011-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-1011-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-1011-01.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/215414/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000032/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-1012-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-1012-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-1012-01.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/215414/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000033/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-1016-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-1016-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-1016-01.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/215414/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000034/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-4591-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-4591-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4591-01.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/215414/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000035/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-4593-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-4593-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4593-01.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/215414/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000036/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-4595-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-4595-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4595-01.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/215414/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000037/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-4599-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-4599-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4599-01.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/215414/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000038/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-4601-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-4601-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4601-01.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/215414/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000039/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-4604-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-4604-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4604-01.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/215414/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000040/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-4607-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-4607-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4607-01.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/215414/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000041/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-4613-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-4613-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-4613-01.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/215414/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000042/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5471-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5471-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5471-01.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/215414/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000043/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5472-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5472-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5472-01.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/215414/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000044/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5473-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5473-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5473-01.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/215414/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000045/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5474-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5474-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5474-01.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/215414/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000046/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5477-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5477-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5477-01.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/215414/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000047/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5478-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5478-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5478-01.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/215414/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000048/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5480-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5480-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5480-01.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/215414/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000049/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5482-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5482-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5482-01.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/215414/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000050/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5485-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5485-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5485-01.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/215414/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000051/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5489-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5489-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5489-01.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/215414/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000052/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5491-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5491-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5491-01.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/215414/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000053/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-22-5492-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-22-5492-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-22-5492-01.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/215414/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000054/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-4532-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-4532-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4532-01.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/215414/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000055/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-4533-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-4533-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4533-01.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/215414/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000056/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-4538-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-4538-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4538-01.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/215414/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000057/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-4547-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-4547-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4547-01.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/215414/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000058/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-4566-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-4566-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4566-01.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/215414/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000059/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-4582-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-4582-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4582-01.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/215414/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000060/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-4583-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-4583-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4583-01.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/215414/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000061/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-4586-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-4586-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-4586-01.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/215414/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000062/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-33-6737-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-33-6737-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-33-6737-01.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/215414/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000063/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-2596-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-2596-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-2596-01.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/215414/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000064/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-2600-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-2600-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-2600-01.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/215414/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000065/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-2608-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-2608-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-2608-01.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/215414/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000066/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5231-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5231-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5231-01.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/215414/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000067/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5232-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5232-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5232-01.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/215414/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000068/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5234-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5234-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5234-01.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/215414/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000069/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5236-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5236-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5236-01.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/215414/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000070/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5239-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5239-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5239-01.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/215414/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000071/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5240-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5240-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5240-01.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/215414/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000072/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5241-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5241-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5241-01.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/215414/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000073/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5927-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5927-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5927-01.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/215414/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000074/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5928-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5928-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5928-01.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/215414/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000075/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-34-5929-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-34-5929-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-34-5929-01.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/215414/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000076/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-37-3783-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-37-3783-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-3783-01.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/215414/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000077/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-37-3789-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-37-3789-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-3789-01.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/215414/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000078/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-37-4133-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-37-4133-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-4133-01.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/215414/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000079/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-37-4135-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-37-4135-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-4135-01.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/215414/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000080/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-37-4141-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-37-4141-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-4141-01.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/215414/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000081/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-37-5819-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-37-5819-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-37-5819-01.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/215414/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000082/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5016-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5016-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5016-01.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/215414/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000083/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5019-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5019-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5019-01.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/215414/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000084/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5021-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5021-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5021-01.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/215414/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000085/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5022-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5022-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5022-01.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/215414/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000086/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5024-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5024-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5024-01.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/215414/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000087/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5027-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5027-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5027-01.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/215414/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000088/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5028-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5028-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5028-01.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/215414/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000089/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5029-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5029-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5029-01.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/215414/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000090/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5030-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5030-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5030-01.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/215414/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000091/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5031-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5031-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5031-01.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/215414/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000092/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5035-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5035-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5035-01.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/215414/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000093/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5036-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5036-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5036-01.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/215414/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000094/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5037-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5037-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5037-01.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/215414/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000095/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-39-5039-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-39-5039-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-39-5039-01.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/215414/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000096/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-43-2578-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-43-2578-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-2578-01.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/215414/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000097/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-43-3394-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-43-3394-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-3394-01.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/215414/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000098/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-43-3920-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-43-3920-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-3920-01.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/215414/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000099/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-43-5668-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-43-5668-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-5668-01.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/215414/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000100/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-43-6143-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-43-6143-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-6143-01.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/215414/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000101/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-43-6647-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-43-6647-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-6647-01.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/215414/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000102/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-43-6770-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-43-6770-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-6770-01.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/215414/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000103/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-43-6771-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-43-6771-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-43-6771-01.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/215414/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000104/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-46-3765-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-46-3765-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3765-01.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/215414/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000105/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-46-3766-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-46-3766-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3766-01.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/215414/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000106/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-46-3767-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-46-3767-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3767-01.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/215414/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000107/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-46-3768-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-46-3768-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3768-01.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/215414/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000108/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-46-3769-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-46-3769-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-3769-01.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/215414/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000109/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-46-6025-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-46-6025-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-6025-01.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/215414/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000110/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-46-6026-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-46-6026-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-46-6026-01.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/215414/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000111/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-51-4079-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-51-4079-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-51-4079-01.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/215414/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000112/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-51-4080-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-51-4080-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-51-4080-01.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/215414/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000113/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-51-4081-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-51-4081-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-51-4081-01.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/215414/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000114/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-56-1622-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-56-1622-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-1622-01.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/215414/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000115/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-56-5897-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-56-5897-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-5897-01.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/215414/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000116/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-56-5898-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-56-5898-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-5898-01.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/215414/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000117/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-56-6545-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-56-6545-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-6545-01.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/215414/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000118/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-56-6546-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-56-6546-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-56-6546-01.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/215414/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000119/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2698-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2698-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2698-01.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/215414/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000120/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2707-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2707-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2707-01.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/215414/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000121/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2708-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2708-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2708-01.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/215414/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000122/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2709-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2709-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2709-01.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/215414/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000123/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2710-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2710-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2710-01.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/215414/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000124/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2711-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2711-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2711-01.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/215414/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000125/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2712-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2712-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2712-01.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/215414/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000126/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2713-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2713-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2713-01.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/215414/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000127/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2715-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2715-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2715-01.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/215414/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000128/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2719-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2719-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2719-01.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/215414/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000129/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2720-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2720-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2720-01.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/215414/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000130/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2721-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2721-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2721-01.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/215414/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000131/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2722-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2722-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2722-01.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/215414/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000132/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2723-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2723-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2723-01.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/215414/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000133/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2724-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2724-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2724-01.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/215414/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000134/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2725-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2725-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2725-01.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/215414/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000135/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-60-2726-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-60-2726-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-60-2726-01.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/215414/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000136/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-63-5128-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-63-5128-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-63-5128-01.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/215414/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000137/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-63-5131-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-63-5131-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-63-5131-01.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/215414/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000138/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-63-6202-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-63-6202-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-63-6202-01.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/215414/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000139/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2727-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2727-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2727-01.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/215414/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000140/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2734-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2734-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2734-01.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/215414/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000141/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2742-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2742-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2742-01.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/215414/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000142/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2744-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2744-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2744-01.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/215414/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000143/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2754-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2754-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2754-01.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/215414/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000144/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2755-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2755-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2755-01.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/215414/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000145/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2756-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2756-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2756-01.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/215414/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000146/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2757-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2757-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2757-01.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/215414/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000147/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2758-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2758-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2758-01.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/215414/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000148/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2759-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2759-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2759-01.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/215414/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000149/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2763-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2763-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2763-01.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/215414/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000150/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2765-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2765-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2765-01.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/215414/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000151/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2766-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2766-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2766-01.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/215414/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000152/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2767-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2767-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2767-01.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/215414/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000153/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2768-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2768-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2768-01.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/215414/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000154/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2770-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2770-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2770-01.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/215414/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000155/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2771-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2771-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2771-01.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/215414/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000156/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2773-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2773-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2773-01.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/215414/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000157/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2777-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2777-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2777-01.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/215414/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000158/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2778-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2778-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2778-01.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/215414/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000159/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2780-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2780-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2780-01.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/215414/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000160/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2781-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2781-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2781-01.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/215414/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000161/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2782-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2782-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2782-01.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/215414/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000162/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2783-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2783-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2783-01.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/215414/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000163/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2785-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2785-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2785-01.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/215414/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000164/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2786-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2786-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2786-01.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/215414/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000165/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2787-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2787-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2787-01.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/215414/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000166/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2788-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2788-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2788-01.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/215414/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000167/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2789-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2789-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2789-01.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/215414/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000168/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2791-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2791-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2791-01.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/215414/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000169/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2792-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2792-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2792-01.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/215414/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000170/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2793-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2793-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2793-01.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/215414/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000171/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2794-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2794-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2794-01.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/215414/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000172/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2795-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2795-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2795-01.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/215414/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000173/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-66-2800-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-66-2800-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-66-2800-01.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/215414/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000174/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-70-6722-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-70-6722-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-70-6722-01.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/215414/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000175/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-70-6723-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-70-6723-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-70-6723-01.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/215414/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000176/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-85-6175-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-85-6175-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-85-6175-01.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/215414/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000177/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-85-6560-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-85-6560-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-85-6560-01.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/215414/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215414/iteration1/scatter.0000000178/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_215414   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "LUSC-85-6561-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "LUSC-85-6561-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/lusc/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.2.9.0/TCGA-85-6561-01.wig.txt"

Finished submitting scatter jobs at Wed Oct 24 15:07:12 2012 in 3.35673346917 minutes
calling:  bsub -E cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -q cga -R select[tmp>1000 && scratch>1] -e scatter-gather.err.txt -o scatter-gather.out.txt -w ended(scatter_215414) -J gather_215414 -P Firehose -R rusage[mem=12] -sp 65   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/run_matlab.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ fh_MutSigCoverageGather   "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/" "LUSC" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/0.MutSigPreprocess.Finished/LUSC.maf" "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "4" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LUSC/1910331/0.MutSigPreprocess.Finished/LUSC.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_215414) -J iteration_215414 -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 215414 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
Path iteration1 exists:  True
