calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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/THCA/1911605/0.MutSigPreprocess.Finished/THCA.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/THCA/1911605/0.MutSigPreprocess.Finished/THCA.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/THCA/1911605/0.MutSigPreprocess.Finished/THCA.maf
Started submitting scatter jobs at Wed Oct 24 16:11:05 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/216198/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0YZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0YZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0YZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0Z0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0Z0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0Z0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0Z2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0Z2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0Z2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0Z3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0Z3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0Z3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0Z5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0Z5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0Z5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0Z9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0Z9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0Z9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0ZA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0ZA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0ZA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0ZB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0ZB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0ZB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0ZC-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0ZC-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0ZC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0ZE-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0ZE-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0ZE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0ZF-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0ZF-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0ZF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0ZG-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0ZG-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0ZG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0ZH-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0ZH-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0ZH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A0ZJ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A0ZJ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A0ZJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A18Y-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A18Y-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A18Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A18Z-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A18Z-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A18Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A190-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A190-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A190-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A191-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A191-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A191-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A192-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A192-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A192-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A28R-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A28R-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A28R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A28S-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A28S-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A28S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A28T-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A28T-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A28T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A28V-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A28V-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A28V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A28X-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A28X-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A28X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A28Z-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A28Z-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A28Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A290-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A290-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A290-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A2N7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A2N7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A2N7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A2N8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A2N8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A2N8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A2N9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A2N9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A2N9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A2NA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A2NA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A2NA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A2P4-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A2P4-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A2P4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A3EZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A3EZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A3EZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A3F0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A3F0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A3F0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A3PR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A3PR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A3PR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A3PT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A3PT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A3PT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-BJ-A3PU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-BJ-A3PU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BJ-A3PU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-CE-A13K-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-CE-A13K-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-CE-A13K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-CE-A27D-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-CE-A27D-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-CE-A27D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-CE-A3MD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-CE-A3MD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-CE-A3MD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-CE-A3ME-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-CE-A3ME-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-CE-A3ME-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DE-A0XZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DE-A0XZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DE-A0XZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DE-A0Y2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DE-A0Y2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DE-A0Y2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DE-A0Y3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DE-A0Y3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DE-A0Y3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DE-A2OL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DE-A2OL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DE-A2OL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DE-A3KN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DE-A3KN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DE-A3KN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13L-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13L-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13M-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13M-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13O-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13O-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13P-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13P-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13R-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13R-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13S-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13S-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13T-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13T-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13U-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13U-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13V-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13V-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13W-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13W-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A13X-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A13X-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A13X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QE-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QE-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QF-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QF-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QG-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QG-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QH-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QH-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QI-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QI-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A1QQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A1QQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A1QQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2PZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2PZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2PZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q4-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q4-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2Q9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2Q9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2Q9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2QA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2QA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2QA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2QB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2QB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2QB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A2QC-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A2QC-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A2QC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UK-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UK-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3US-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3US-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3US-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DJ-A3UY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DJ-A3UY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DJ-A3UY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DO-A1JZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DO-A1JZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DO-A1JZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DO-A1K0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DO-A1K0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DO-A1K0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-DO-A2HM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-DO-A2HM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DO-A2HM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E3-A3DY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E3-A3DY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E3-A3DY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E3-A3DZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E3-A3DZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E3-A3DZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E3-A3E0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E3-A3E0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E3-A3E0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E3-A3E1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E3-A3E1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E3-A3E1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E3-A3E2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E3-A3E2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E3-A3E2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E3-A3E3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E3-A3E3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E3-A3E3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E3-A3E5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E3-A3E5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E3-A3E5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E8-A242-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E8-A242-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E8-A242-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-E8-A2EA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-E8-A2EA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-E8-A2EA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3CZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3CZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3CZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3D0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3D0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3D0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3D1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3D1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3D1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3D4-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3D4-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3D4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3D5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3D5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3D5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3D6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3D6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3D6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3GZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3GZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3GZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3H1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3H1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3H1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3H2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3H2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3H2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3H3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3H3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3H3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3H4-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3H4-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3H4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3H5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3H5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3H5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3H7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3H7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3H7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3H8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3H8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3H8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3MW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3MW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3MW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3MX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3MX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3MX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3MY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3MY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3MY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3MZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3MZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3MZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3N2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3N2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3N2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3N3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3N3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3N3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3T0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3T0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3T0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3T1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3T1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3T1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3T2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3T2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3T2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3T3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3T3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3T3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3T6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3T6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3T6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3T7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3T7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3T7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3T8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3T8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3T8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3T9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3T9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3T9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3TA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3TA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3TA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EL-A3TB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EL-A3TB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EL-A3TB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1CS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1CS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1CS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1CT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1CT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1CT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1CU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1CU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1CU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1CV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1CV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1CV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1CW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1CW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1CW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1YA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1YA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1YA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000179 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000179/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1YB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1YB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1YB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000180 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000180/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1YC-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1YC-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1YC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000181 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000181/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1YD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1YD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1YD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000182 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000182/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A1YE-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A1YE-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A1YE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000183 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000183/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22I-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22I-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000184 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000184/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22J-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22J-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000185 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000185/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22K-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22K-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000186 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000186/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22L-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22L-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000187 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000187/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22M-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22M-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000188 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000188/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22N-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22N-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000189 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000189/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22O-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22O-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000190 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000190/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22P-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22P-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000191 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000191/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A22Q-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A22Q-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A22Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000192 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000192/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CJ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CJ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000193 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000193/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CK-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CK-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000194 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000194/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000195 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000195/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000196 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000196/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000197 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000197/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000198 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000198/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000199 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000199/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000200 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000200/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000201 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000201/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000202 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000202/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2CU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2CU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2CU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000203 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000203/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2OV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2OV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2OV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000204 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000204/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2OW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2OW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2OW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000205 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000205/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2OX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2OX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2OX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000206 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000206/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2OY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2OY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2OY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000207 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000207/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2P0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2P0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2P0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000208 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000208/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2P1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2P1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2P1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000209 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000209/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2P2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2P2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2P2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000210 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000210/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A2P3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A2P3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A2P3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000211 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000211/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AI-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AI-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000212 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000212/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AJ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AJ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000213 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000213/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AK-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AK-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000214 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000214/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000215 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000215/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000216 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000216/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000217 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000217/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000218 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000218/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000219 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000219/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3AR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3AR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3AR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000220 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000220/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FJ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FJ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000221 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000221/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FK-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FK-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000222 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000222/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000223 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000223/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000224 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000224/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000225 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000225/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000226 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000226/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000227 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000227/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000228 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000228/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3FR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3FR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3FR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000229 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000229/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3O3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3O3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3O3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000230 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000230/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3O6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3O6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3O6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000231 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000231/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3O7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3O7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3O7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000232 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000232/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3O8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3O8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3O8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000233 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000233/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3O9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3O9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3O9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000234 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000234/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3OA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3OA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3OA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000235 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000235/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-EM-A3OB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-EM-A3OB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EM-A3OB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000236 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000236/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A25G-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A25G-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A25G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000237 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000237/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A25I-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A25I-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A25I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000238 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000238/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A25J-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A25J-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A25J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000239 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000239/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A25K-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A25K-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A25K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000240 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000240/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A25O-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A25O-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A25O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000241 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000241/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A25R-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A25R-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A25R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000242 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000242/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A2MY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A2MY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A2MY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000243 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000243/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A2MZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A2MZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A2MZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000244 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000244/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A2N0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A2N0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A2N0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000245 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000245/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A2N1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A2N1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A2N1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000246 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000246/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A2N4-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A2N4-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A2N4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000247 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000247/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A2N5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A2N5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A2N5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000248 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000248/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39I-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39I-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000249 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000249/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39J-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39J-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000250 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000250/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39K-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39K-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000251 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000251/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39L-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39L-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000252 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000252/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39M-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39M-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000253 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000253/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39N-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39N-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000254 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000254/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39O-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39O-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000255 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000255/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39P-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39P-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000256 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000256/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39R-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39R-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000257 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000257/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39S-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39S-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000258 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000258/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A39T-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A39T-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A39T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000259 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000259/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000260 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000260/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000261 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000261/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000262 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000262/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000263 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000263/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000264 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000264/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000265 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000265/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000266 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000266/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000267 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000267/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000268 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000268/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3BX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3BX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3BX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000269 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000269/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000270 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000270/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000271 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000271/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000272 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000272/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000273 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000273/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000274 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000274/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000275 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000275/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000276 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000276/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000277 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000277/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-ET-A3DW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-ET-A3DW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-ET-A3DW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000278 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000278/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A22Z-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A22Z-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A22Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000279 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000279/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A230-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A230-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A230-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000280 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000280/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A231-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A231-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A231-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000281 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000281/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A232-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A232-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A232-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000282 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000282/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A233-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A233-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A233-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000283 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000283/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A234-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A234-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A234-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000284 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000284/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A235-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A235-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A235-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000285 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000285/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A236-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A236-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A236-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000286 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000286/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A237-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A237-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A237-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000287 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000287/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A23A-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A23A-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A23A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000288 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000288/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A3PB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A3PB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A3PB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000289 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000289/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A3PC-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A3PC-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A3PC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000290 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000290/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FE-A3PD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FE-A3PD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FE-A3PD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000291 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000291/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FK-A3S3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FK-A3S3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FK-A3S3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000292 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000292/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FK-A3SB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FK-A3SB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FK-A3SB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000293 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000293/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FK-A3SD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FK-A3SD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FK-A3SD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000294 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000294/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FK-A3SE-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FK-A3SE-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FK-A3SE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000295 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000295/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FK-A3SG-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FK-A3SG-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FK-A3SG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000296 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000296/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FK-A3SH-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FK-A3SH-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FK-A3SH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000297 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000297/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A2QD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A2QD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A2QD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000298 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000298/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3BL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3BL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3BL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000299 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000299/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3I4-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3I4-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3I4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000300 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000300/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3I5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3I5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3I5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000301 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000301/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3NM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3NM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3NM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000302 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000302/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3NN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3NN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3NN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000303 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000303/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3NP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3NP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3NP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000304 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000304/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3ON-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3ON-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3ON-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000305 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000305/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3R6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3R6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3R6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000306 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000306/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3R7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3R7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3R7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000307 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000307/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3R8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3R8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3R8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000308 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000308/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3R9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3R9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3R9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000309 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000309/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3RA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3RA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3RA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000310 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000310/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3W9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3W9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3W9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000311 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000311/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-FY-A3WA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-FY-A3WA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-FY-A3WA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000312 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000312/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-GE-A2C6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-GE-A2C6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-GE-A2C6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000313 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000313/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-H2-A26U-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-H2-A26U-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-H2-A26U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000314 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000314/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-H2-A2K9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-H2-A2K9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-H2-A2K9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000315 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000315/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-H2-A3RH-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-H2-A3RH-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-H2-A3RH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000316 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000316/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-H2-A3RI-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-H2-A3RI-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-H2-A3RI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000317 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000317/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-IM-A3EB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-IM-A3EB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-IM-A3EB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000318 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000318/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-IM-A3ED-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-IM-A3ED-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-IM-A3ED-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000319 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000319/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-IM-A3U2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-IM-A3U2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-IM-A3U2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000320 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000320/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-IM-A3U3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-IM-A3U3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-IM-A3U3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000321 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000321/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-J8-A3NZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-J8-A3NZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-J8-A3NZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000322 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000322/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-J8-A3O0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-J8-A3O0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-J8-A3O0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000323 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216198/iteration1/scatter.0000000323/*; 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_216198   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "THCA-J8-A3O1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "THCA-J8-A3O1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/thca/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-J8-A3O1-01.wig.txt"

Finished submitting scatter jobs at Wed Oct 24 16:14:47 2012 in 3.69994606972 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_216198) -J gather_216198 -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/" "THCA" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/THCA/1911605/0.MutSigPreprocess.Finished/THCA.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/THCA/1911605/0.MutSigPreprocess.Finished/THCA.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_216198) -J iteration_216198 -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 216198 --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
