calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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/KIRP-TP/2283891/0.MutSigPreprocess.Finished/KIRP-TP.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/KIRP-TP/2283891/0.MutSigPreprocess.Finished/KIRP-TP.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/KIRP-TP/2283891/0.MutSigPreprocess.Finished/KIRP-TP.maf
Started submitting scatter jobs at Thu Jan 10 14:40:47 2013
calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7286-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7286-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7286-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7287-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7287-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7287-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7288-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7288-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7288-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7583-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7583-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7583-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7584-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7584-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7584-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7585-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7585-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7585-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7732-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7732-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7732-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7734-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7734-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7734-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7828-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7828-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7828-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7915-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7915-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7915-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7996-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7996-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7996-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-A4-7997-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-A4-7997-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7997-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-AL-3466-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-AL-3466-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3466-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-AL-3467-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-AL-3467-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3467-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-AL-3468-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-AL-3468-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3468-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-AL-3472-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-AL-3472-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3472-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-AL-3473-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-AL-3473-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3473-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-AL-7173-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-AL-7173-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-7173-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B1-5398-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B1-5398-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B1-5398-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B3-3925-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B3-3925-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B3-3925-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B3-3926-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B3-3926-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B3-3926-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B3-4103-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B3-4103-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B3-4103-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B3-4104-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B3-4104-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B3-4104-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-4113-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-4113-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4113-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-4114-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-4114-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4114-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-4115-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-4115-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4115-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-4116-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-4116-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4116-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-4117-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-4117-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4117-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-4617-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-4617-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4617-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-5155-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-5155-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-5155-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-5156-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-5156-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-5156-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-B9-7268-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-B9-7268-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-7268-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5875-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5875-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5875-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5876-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5876-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5876-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5877-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5877-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5877-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5878-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5878-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5878-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5879-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5879-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5879-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5880-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5880-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5880-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5881-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5881-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5881-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5882-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5882-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5882-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5883-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5883-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5883-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5884-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5884-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5884-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5885-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5885-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5885-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5886-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5886-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5886-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5887-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5887-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5887-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5888-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5888-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5888-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5889-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5889-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5889-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5890-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5890-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5890-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5891-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5891-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5891-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5892-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5892-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5892-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5893-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5893-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5893-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-5894-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-5894-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5894-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7044-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7044-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7044-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7045-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7045-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7045-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7046-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7046-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7046-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7048-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7048-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7048-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7049-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7049-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7049-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7050-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7050-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7050-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7051-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7051-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7051-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7053-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7053-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7053-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7055-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7055-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7055-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7056-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7056-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7056-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7058-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7058-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7058-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7059-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7059-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7059-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7060-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7060-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7060-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7061-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7061-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7061-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-BQ-7062-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-BQ-7062-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7062-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-5560-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-5560-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-5560-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-5561-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-5561-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-5561-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-7834-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-7834-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7834-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-7837-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-7837-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7837-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-7838-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-7838-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7838-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-7839-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-7839-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7839-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-7840-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-7840-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7840-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-7841-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-7841-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7841-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DW-7842-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DW-7842-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7842-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DZ-6131-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DZ-6131-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6131-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DZ-6132-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DZ-6132-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6132-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DZ-6133-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DZ-6133-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6133-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DZ-6134-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DZ-6134-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6134-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-DZ-6135-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-DZ-6135-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6135-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-EV-5901-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-EV-5901-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EV-5901-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-EV-5902-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-EV-5902-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EV-5902-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-EV-5903-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-EV-5903-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EV-5903-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-6789-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-6789-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6789-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-6790-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-6790-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6790-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-6792-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-6792-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6792-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-6793-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-6793-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6793-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-6795-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-6795-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6795-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-6796-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-6796-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6796-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-6797-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-6797-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6797-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-7501-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-7501-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-7501-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-G7-7502-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-G7-7502-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-7502-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-GL-6846-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-GL-6846-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-GL-6846-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-GL-7773-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-GL-7773-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-GL-7773-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-GL-7966-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-GL-7966-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-GL-7966-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-HE-7128-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-HE-7128-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-HE-7128-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-HE-7129-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-HE-7129-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-HE-7129-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-HE-7130-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-HE-7130-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-HE-7130-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/285912/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_285912   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "KIRP-J7-6720-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "KIRP-J7-6720-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-J7-6720-01.wig.txt"

Finished submitting scatter jobs at Thu Jan 10 14:42:09 2013 in 1.36678593159 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_285912) -J gather_285912 -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/" "KIRP-TP" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/KIRP-TP/2283891/0.MutSigPreprocess.Finished/KIRP-TP.maf" "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "4" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/KIRP-TP/2283891/0.MutSigPreprocess.Finished/KIRP-TP.patients.txt"

calling:  bsub -E cd "/xchip/cga" -q cga -R select[tmp>1000 && scratch>1] -e iterator.err.txt -o iterator.out.txt -w ended(gather_285912) -J iteration_285912 -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 285912 --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
