calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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/BRCA/1780791/0.MutSigPreprocess.Finished/BRCA.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BRCA/1780791/0.MutSigPreprocess.Finished/BRCA.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BRCA/1780791/0.MutSigPreprocess.Finished/BRCA.maf
Started submitting scatter jobs at Fri Oct  5 15:48:51 2012
calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A1-A0SD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A1-A0SD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A1-A0SD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A1-A0SE" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A1-A0SE.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A1-A0SE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A1-A0SH" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A1-A0SH.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A1-A0SH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A1-A0SJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A1-A0SJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A1-A0SJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A1-A0SK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A1-A0SK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A1-A0SK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A1-A0SM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A1-A0SM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A1-A0SM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A1-A0SO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A1-A0SO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A1-A0SO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04N" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04N.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04Q" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04Q.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04U" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04U.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04V" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04V.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04W" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04W.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04X" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04X.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A04Y" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A04Y.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A04Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0CZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0CZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0CZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0D0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0D0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0D0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0D1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0D1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0D1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0D2" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0D2.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0D2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0D3" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0D3.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0D3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0D4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0D4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0D4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0ER" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0ER.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0ER-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0ES" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0ES.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0ES-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0ET" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0ET.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0ET-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0EY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0EY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0EY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0ST" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0ST.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0ST-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0SU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0SU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0SU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0SV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0SV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0SV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0SW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0SW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0SW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0SX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0SX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0SX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0SY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0SY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0SY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0T0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0T0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0T0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0T1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0T1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0T1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0T2" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0T2.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0T2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0T3" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0T3.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0T3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0T4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0T4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0T4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0T6" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0T6.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0T6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0T7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0T7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0T7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YC" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YC.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YF" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YF.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YG" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YG.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YH" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YH.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A2-A0YM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A2-A0YM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A2-A0YM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A0CD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A0CD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A0CD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A0CE" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A0CE.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A0CE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A0CG" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A0CG.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A0CG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A0CH" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A0CH.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A0CH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A0CJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A0CJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A0CJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A0D9" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A0D9.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A0D9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A0DA" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A0DA.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A0DA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A0DB" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A0DB.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A0DB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A13D" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A13D.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A13D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A7-A13F" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A7-A13F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A7-A13F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06N" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06N.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06O" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06Q" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06Q.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06T" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06U" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06U.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06X" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06X.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06Y" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06Y.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A06Z" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A06Z.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A06Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A075" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A075.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A075-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A076" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A076.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A076-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A079" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A079.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A079-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07B" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07B.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07C" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07C.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07E" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07E.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07E-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07F" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07G" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07G.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07I" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07I.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07J" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07J.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07L" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07O" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07U" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07U.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07W" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07W.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A07Z" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A07Z.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A07Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A081" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A081.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A081-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A082" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A082.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A082-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A083" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A083.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A083-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A084" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A084.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A084-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A085" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A085.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A085-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A086" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A086.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A086-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08A" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08A.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08B" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08B.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08C" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08C.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08F" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08G" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08G.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08H" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08H.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08I" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08I.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08J" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08J.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08L" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08O" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08T" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08X" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08X.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A08Z" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A08Z.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A08Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A090" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A090.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A090-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A091" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A091.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A091-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A092" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A092.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A092-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A093" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A093.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A093-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A094" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A094.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A094-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A095" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A095.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A095-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A096" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A096.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A096-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A097" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A097.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A097-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A099" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A099.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A099-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09A" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09A.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09B" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09B.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09C" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09C.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09D" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09D.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09G" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09G.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09I" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09I.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09M" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09M.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09N" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09N.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09Q" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09Q.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09T" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09V" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09V.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09W" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09W.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A09X" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A09X.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A09X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A0A1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A0A1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A0A1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A0A2" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A0A2.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A0A2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A0A4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A0A4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A0A4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A0A7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A0A7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A0A7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A0A9" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A0A9.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A0A9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A0AB" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A0AB.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A0AB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-A8-A0AD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-A8-A0AD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-A8-A0AD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A03X" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A03X.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A03X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A03Y" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A03Y.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A03Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A041" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A041.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A041-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A049" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A049.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A049-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A04A" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A04A.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A04A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A04C" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A04C.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A04C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A04D" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A04D.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A04D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0AJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0AJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0AJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0AL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0AL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0AL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0AM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0AM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0AM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0AR" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0AR.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0AR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0AS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0AS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0AS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0AT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0AT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0AT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FF" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FF.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000179 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000180 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000181 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0FZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0FZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0FZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000182 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0G0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0G0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0G0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000183 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000184 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000185 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000186 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000187 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XR" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XR.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000188 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000189 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000190 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000191 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000192 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AN-A0XW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AN-A0XW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AN-A0XW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000193 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A03L" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A03L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A03L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000194 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A03N" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A03N.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A03N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000195 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A03O" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A03O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A03O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000196 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A03P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A03P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A03P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000197 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A03R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A03R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A03R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000198 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A03T" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A03T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A03T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000199 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A03U" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A03U.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A03U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000200 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A03V" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A03V.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A03V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000201 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0J2" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0J2.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0J2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000202 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0J3" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0J3.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0J3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000203 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0J4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0J4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0J4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000204 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0J6" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0J6.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0J6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000205 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0J7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0J7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0J7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000206 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0J8" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0J8.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0J8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000207 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0J9" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0J9.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0J9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000208 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JA" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JA.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000209 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JB" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JB.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000210 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JC" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JC.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000211 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000212 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JE" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JE.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000213 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JF" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JF.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000214 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JG" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JG.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000215 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000216 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000217 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000218 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A0JM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A0JM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A0JM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000219 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A124" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A124.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A124-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000220 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A125" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A125.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A125-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000221 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A126" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A126.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A126-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000222 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A129" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A129.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A129-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000223 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A12A" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A12A.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A12A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000224 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A12B" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A12B.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A12B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000225 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A12D" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A12D.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A12D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000226 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A12E" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A12E.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A12E-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000227 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A12F" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A12F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A12F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000228 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A12G" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A12G.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A12G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000229 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AO-A12H" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AO-A12H.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AO-A12H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000230 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AQ-A04H" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AQ-A04H.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AQ-A04H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000231 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AQ-A04J" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AQ-A04J.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AQ-A04J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000232 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AQ-A04L" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AQ-A04L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AQ-A04L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000233 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000234 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000235 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TR" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TR.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000236 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000237 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000238 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000239 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000240 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000241 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000242 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000243 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0TZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0TZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0TZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000244 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0U0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0U0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0U0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000245 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0U1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0U1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0U1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000246 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0U2" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0U2.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0U2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000247 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0U3" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0U3.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0U3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000248 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A0U4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A0U4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A0U4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000249 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AH" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AH.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000250 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000251 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000252 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000253 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000254 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000255 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000256 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000257 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000258 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AR" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AR.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000259 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000260 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000261 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000262 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000263 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000264 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000265 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-AR-A1AY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-AR-A1AY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-AR-A1AY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000266 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0I2" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0I2.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0I2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000267 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0I5" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0I5.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0I5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000268 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0I6" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0I6.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0I6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000269 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0I8" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0I8.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0I8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000270 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0I9" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0I9.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0I9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000271 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IA" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IA.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000272 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IB" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IB.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000273 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IC" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IC.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000274 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IE" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IE.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000275 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IG" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IG.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000276 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IH" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IH.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000277 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000278 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000279 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000280 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000281 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000282 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000283 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0IQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0IQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0IQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000284 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RE" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RE.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000285 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RG" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RG.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000286 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RH" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RH.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000287 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000288 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000289 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000290 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000291 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000292 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000293 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000294 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000295 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000296 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000297 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0RV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0RV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0RV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000298 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0WS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0WS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0WS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000299 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0WT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0WT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0WT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000300 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0WV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0WV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0WV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000301 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0WW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0WW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0WW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000302 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0WX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0WX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0WX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000303 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0WY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0WY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0WY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000304 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0WZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0WZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0WZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000305 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0X0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0X0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0X0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000306 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0X1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0X1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0X1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000307 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0X4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0X4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0X4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000308 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0X5" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0X5.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0X5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000309 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-B6-A0X7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-B6-A0X7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-B6-A0X7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000310 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0AU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0AU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0AU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000311 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0AV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0AV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0AV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000312 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0AW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0AW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0AW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000313 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0AY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0AY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0AY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000314 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0AZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0AZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0AZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000315 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0B0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0B0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0B0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000316 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0B1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0B1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0B1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000317 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0B3" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0B3.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0B3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000318 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0B4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0B4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0B4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000319 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0B5" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0B5.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0B5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000320 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0B7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0B7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0B7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000321 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0B8" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0B8.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0B8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000322 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0B9" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0B9.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0B9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000323 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/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_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BA" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BA.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000324 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000324/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BC" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BC.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000325 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000325/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000326 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000326/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BF" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BF.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000327 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000327/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BG" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BG.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000328 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000328/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BJ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BJ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000329 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000329/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000330 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000330/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000331 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000331/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000332 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000332/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000333 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000333/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000334 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000334/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BR" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BR.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000335 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000335/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000336 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000336/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000337 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000337/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000338 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000338/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000339 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000339/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0BZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0BZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0BZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000340 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000340/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0C0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0C0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0C0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000341 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000341/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0C1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0C1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0C1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000342 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000342/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0C3" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0C3.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0C3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000343 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000343/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0C7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0C7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0C7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000344 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000344/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000345 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000345/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DE" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DE.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000346 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000346/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DG" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DG.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000347 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000347/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DH" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DH.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000348 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000348/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000349 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000349/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000350 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000350/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000351 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000351/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000352 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000352/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000353 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000353/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000354 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000354/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DS" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DS.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000355 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000355/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DT" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DT.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000356 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000356/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000357 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000357/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000358 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000358/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0DZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0DZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0DZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000359 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000359/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0E0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0E0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0E0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000360 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000360/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0E1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0E1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0E1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000361 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000361/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0E2" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0E2.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0E2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000362 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000362/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0E6" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0E6.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0E6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000363 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000363/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0E7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0E7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0E7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000364 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000364/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0E9" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0E9.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0E9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000365 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000365/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0EA" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0EA.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0EA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000366 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000366/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0EB" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0EB.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0EB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000367 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000367/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0EE" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0EE.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0EE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000368 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000368/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0EI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0EI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0EI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000369 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000369/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0GY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0GY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0GY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000370 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000370/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0GZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0GZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0GZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000371 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000371/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0H0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0H0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0H0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000372 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000372/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0H3" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0H3.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0H3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000373 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000373/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0H5" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0H5.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0H5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000374 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000374/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0H6" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0H6.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0H6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000375 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000375/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0H7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0H7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0H7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000376 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000376/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0H9" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0H9.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0H9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000377 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000377/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HA" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HA.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000378 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000378/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HB" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HB.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000379 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000379/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000380 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000380/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HK" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HK.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HK-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000381 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000381/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000382 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000382/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000383 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000383/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000384 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000384/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000385 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000385/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HQ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HQ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000386 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000386/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000387 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000387/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000388 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000388/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000389 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000389/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0HY" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0HY.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0HY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000390 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000390/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0RX" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0RX.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0RX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000391 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000391/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0W3" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0W3.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0W3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000392 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000392/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0W4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0W4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0W4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000393 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000393/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0W5" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0W5.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0W5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000394 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000394/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0W7" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0W7.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0W7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000395 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000395/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A0WA" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A0WA.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A0WA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000396 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000396/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18F" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000397 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000397/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18H" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18H.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000398 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000398/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18I" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18I.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000399 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000399/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18J" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18J.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000400 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000400/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18K" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18K.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000401 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000401/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18L" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000402 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000402/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18M" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18M.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000403 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000403/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18N" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18N.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000404 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000404/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000405 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000405/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18Q" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18Q.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000406 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000406/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000407 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000407/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18S" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18S.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000408 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000408/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18T" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000409 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000409/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18U" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18U.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000410 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000410/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A18V" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A18V.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A18V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000411 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000411/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A1EO" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A1EO.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A1EO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000412 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000412/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A1ES" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A1ES.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A1ES-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000413 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000413/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A1ET" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A1ET.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A1ET-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000414 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000414/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A1EU" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A1EU.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A1EU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000415 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000415/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A1EV" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A1EV.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A1EV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000416 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000416/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A1EW" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A1EW.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A1EW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000417 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000417/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-BH-A1F0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-BH-A1F0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-BH-A1F0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000418 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000418/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12K" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12K.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000419 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000419/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12L" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000420 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000420/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12M" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12M.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000421 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000421/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12N" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12N.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000422 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000422/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12O" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000423 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000423/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000424 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000424/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12Q" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12Q.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000425 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000425/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12T" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000426 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000426/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12U" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12U.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000427 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000427/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12V" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12V.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000428 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000428/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12W" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12W.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000429 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000429/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12X" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12X.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000430 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000430/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12Y" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12Y.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000431 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000431/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A12Z" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A12Z.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A12Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000432 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000432/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A130" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A130.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A130-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000433 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000433/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A131" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A131.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A131-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000434 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000434/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A132" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A132.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A132-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000435 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000435/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A133" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A133.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A133-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000436 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000436/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A134" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A134.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A134-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000437 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000437/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A135" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A135.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A135-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000438 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000438/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A137" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A137.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A137-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000439 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000439/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A138" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A138.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A138-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000440 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000440/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A1HF" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A1HF.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A1HF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000441 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000441/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A1HG" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A1HG.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A1HG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000442 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000442/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A1HI" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A1HI.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A1HI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000443 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000443/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A1HL" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A1HL.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A1HL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000444 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000444/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A1HM" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A1HM.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A1HM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000445 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000445/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-C8-A1HN" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-C8-A1HN.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-C8-A1HN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000446 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000446/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-D8-A13Y" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-D8-A13Y.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-D8-A13Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000447 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000447/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-D8-A13Z" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-D8-A13Z.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-D8-A13Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000448 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000448/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-D8-A140" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-D8-A140.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-D8-A140-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000449 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000449/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-D8-A141" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-D8-A141.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-D8-A141-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000450 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000450/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-D8-A142" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-D8-A142.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-D8-A142-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000451 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000451/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-D8-A143" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-D8-A143.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-D8-A143-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000452 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000452/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-D8-A145" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-D8-A145.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-D8-A145-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000453 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000453/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-D8-A147" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-D8-A147.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-D8-A147-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000454 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000454/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A105" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A105.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A105-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000455 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000455/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A107" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A107.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A107-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000456 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000456/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A108" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A108.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A108-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000457 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000457/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A109" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A109.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A109-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000458 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000458/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A10A" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A10A.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A10A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000459 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000459/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A10B" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A10B.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A10B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000460 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000460/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A10C" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A10C.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A10C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000461 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000461/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A10E" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A10E.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A10E-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000462 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000462/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A10F" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A10F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A10F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000463 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000463/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14N" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14N.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000464 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000464/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14O" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000465 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000465/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000466 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000466/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14Q" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14Q.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000467 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000467/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000468 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000468/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14S" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14S.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000469 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000469/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14T" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000470 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000470/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14V" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14V.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000471 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000471/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14W" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14W.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000472 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000472/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14X" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14X.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000473 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000473/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14Y" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14Y.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000474 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000474/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A14Z" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A14Z.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A14Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000475 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000475/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A150" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A150.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A150-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000476 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000476/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A152" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A152.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A152-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000477 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000477/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A153" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A153.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A153-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000478 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000478/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A154" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A154.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A154-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000479 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000479/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A155" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A155.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A155-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000480 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000480/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A156" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A156.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A156-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000481 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000481/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A158" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A158.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A158-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000482 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000482/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A159" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A159.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A159-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000483 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000483/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15A" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15A.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000484 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000484/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15C" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15C.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000485 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000485/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15D" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15D.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000486 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000486/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15E" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15E.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15E-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000487 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000487/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15F" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15F.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000488 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000488/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15G" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15G.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000489 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000489/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15H" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15H.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000490 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000490/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15I" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15I.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000491 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000491/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15J" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15J.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000492 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000492/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15K" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15K.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000493 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000493/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15L" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15L.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000494 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000494/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15M" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15M.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000495 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000495/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15O" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15O.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000496 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000496/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15P" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15P.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000497 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000497/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15R" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15R.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000498 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000498/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15S" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15S.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000499 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000499/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A15T" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A15T.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A15T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000500 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000500/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A1AZ" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A1AZ.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A1AZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000501 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000501/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A1B0" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A1B0.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A1B0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000502 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000502/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A1B1" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A1B1.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A1B1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000503 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000503/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A1B4" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A1B4.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A1B4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000504 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000504/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A1B5" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A1B5.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A1B5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000505 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000505/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A1B6" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A1B6.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A1B6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000506 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000506/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A1BC" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A1BC.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A1BC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000507 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/177293/iteration1/scatter.0000000507/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_177293   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "BRCA-E2-A1BD" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "BRCA-E2-A1BD.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/brca/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.2.6.0/TCGA-E2-A1BD-01.wig.txt"

Finished submitting scatter jobs at Fri Oct  5 16:03:52 2012 in 15.0190307339 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_177293) -J gather_177293 -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/" "BRCA" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BRCA/1780791/0.MutSigPreprocess.Finished/BRCA.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/BRCA/1780791/0.MutSigPreprocess.Finished/BRCA.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_177293) -J iteration_177293 -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 177293 --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
