calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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/UCEC/1911650/0.MutSigPreprocess.Finished/UCEC.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/UCEC/1911650/0.MutSigPreprocess.Finished/UCEC.patients.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/UCEC/1911650/0.MutSigPreprocess.Finished/UCEC.maf
Started submitting scatter jobs at Wed Oct 24 16:12:55 2012
calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0G3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0G3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0G3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0G5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0G5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0G5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0G9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0G9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0G9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GE-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GE-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GH-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GH-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GI-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GI-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GJ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GJ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0GX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0GX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0GX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0R6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0R6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0R6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0R7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0R7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0R7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0R8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0R8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0R8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0R9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0R9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0R9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0RA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0RA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0RA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0VO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0VO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0VO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0VP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0VP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0VP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-A5-A0VQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-A5-A0VQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-A5-A0VQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AJ-A23M-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AJ-A23M-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AJ-A23M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A051-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A051-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A051-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A052-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A052-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A052-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A053-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A053-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A053-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A054-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A054-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A054-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A056-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A056-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A056-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A059-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A059-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A059-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A05A-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A05A-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A05A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A05D-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A05D-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A05D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A05H-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A05H-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A05H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A05J-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A05J-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A05J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A05N-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A05N-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A05N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A05P-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A05P-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A05P-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0L8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0L8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0L8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0L9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0L9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0L9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LE-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LE-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LF-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LF-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LG-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LG-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LH-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LH-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LI-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LI-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LJ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LJ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A0LV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A0LV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A0LV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AP-A1DQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AP-A1DQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AP-A1DQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A05S-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A05S-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A05S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A05T-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A05T-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A05T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A05U-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A05U-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A05U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A05W-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A05W-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A05W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A05Y-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A05Y-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A05Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A05Z-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A05Z-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A05Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A060-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A060-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A060-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A062-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A062-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A062-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A063-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A063-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A063-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A064-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A064-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A064-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A06B-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A06B-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A06B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A06H-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A06H-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A06H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A06L-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A06L-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A06L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A0IS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A0IS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A0IS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A0IU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A0IU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A0IU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A0IW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A0IW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A0IW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A0J0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A0J0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A0J0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A0J1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A0J1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A0J1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A1C7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A1C7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A1C7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A1C8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A1C8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A1C8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A1CP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A1CP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A1CP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A2H5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A2H5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A2H5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-AX-A2HF-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-AX-A2HF-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-AX-A2HF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0JN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0JN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0JN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0JR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0JR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0JR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0JS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0JS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0JS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0JT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0JT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0JT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0JV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0JV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0JV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0JY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0JY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0JY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0JZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0JZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0JZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K4-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K4-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A0K9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A0K9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A0K9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11E-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11E-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11E-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11F-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11F-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11G-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11G-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/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_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11H-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11H-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000101/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11I-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11I-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000102/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11J-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11J-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000103/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11M-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11M-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000104/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11N-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11N-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000105/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11O-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11O-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000106/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11Q-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11Q-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000107/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11R-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11R-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000108/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11S-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11S-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000109/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11U-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11U-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000110/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11V-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11V-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000111/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11W-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11W-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000112/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11X-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11X-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000113/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11Y-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11Y-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000114/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A11Z-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A11Z-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A11Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000115/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A121-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A121-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A121-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000116/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A1MU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A1MU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A1MU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000117/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-B5-A1MY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-B5-A1MY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-B5-A1MY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000118/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0LW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0LW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0LW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000119/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0LX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0LX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0LX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000120/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0M0-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0M0-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0M0-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000121/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0M2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0M2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0M2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000122/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0M3-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0M3-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0M3-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000123/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0M4-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0M4-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0M4-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000124/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0M6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0M6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0M6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000125/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0M7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0M7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0M7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000126/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0M8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0M8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0M8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000127/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0M9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0M9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0M9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000128/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0MC-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0MC-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0MC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000129/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0MG-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0MG-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0MG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000130/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0MI-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0MI-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0MI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000131/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0MO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0MO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0MO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000132/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0MQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0MQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0MQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000133/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0MS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0MS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0MS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000134/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0MT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0MT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0MT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000135/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0MU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0MU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0MU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000136/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0RY-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0RY-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0RY-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000137/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0VT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0VT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0VT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000138/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0VV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0VV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0VV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000139/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0VW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0VW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0VW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000140/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0VX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0VX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0VX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000141/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0VZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0VZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0VZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000142/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0W1-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0W1-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0W1-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000143/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0W2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0W2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0W2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000144/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0YU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0YU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0YU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000145/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A0YV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A0YV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A0YV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000146/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A186-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A186-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A186-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000147/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A187-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A187-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A187-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000148/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A18A-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A18A-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A18A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000149/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A18B-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A18B-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A18B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000150/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A18C-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A18C-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A18C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000151/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BG-A2AE-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BG-A2AE-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BG-A2AE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000152/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BK-A0C9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BK-A0C9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BK-A0C9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000153/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BK-A0CA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BK-A0CA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BK-A0CA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000154/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BK-A0CB-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BK-A0CB-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BK-A0CB-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000155/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BK-A0CC-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BK-A0CC-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BK-A0CC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000156/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BK-A139-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BK-A139-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BK-A139-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000157/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BK-A13C-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BK-A13C-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BK-A13C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000158/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0T9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0T9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0T9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000159/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0TA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0TA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0TA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000160/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0TC-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0TC-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0TC-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000161/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0TD-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0TD-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0TD-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000162/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0TE-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0TE-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0TE-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000163/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0TG-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0TG-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0TG-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000164/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0TI-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0TI-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0TI-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000165/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0TJ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0TJ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0TJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000166/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0U5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0U5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0U5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000167/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0U7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0U7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0U7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000168/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0U8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0U8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0U8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000169/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0U9-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0U9-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0U9-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000170/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0UA-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0UA-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0UA-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000171/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0UF-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0UF-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0UF-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000172/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0UJ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0UJ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0UJ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000173/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0UL-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0UL-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0UL-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000174/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0UM-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0UM-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0UM-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000175/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0UT-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0UT-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0UT-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000176/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0UV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0UV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0UV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000177/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0V6-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0V6-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0V6-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000178/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0V7-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0V7-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0V7-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000179 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000179/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0V8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0V8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0V8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000180 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000180/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-BS-A0WQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-BS-A0WQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-BS-A0WQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000181 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000181/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000182 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000182/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZO-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZO-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZO-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000183 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000183/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZP-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZP-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZP-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000184 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000184/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZQ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZQ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZQ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000185 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000185/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZR-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZR-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZR-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000186 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000186/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000187 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000187/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000188 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000188/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZV-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZV-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZV-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000189 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000189/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A0ZZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A0ZZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A0ZZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000190 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000190/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A101-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A101-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A101-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000191 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000191/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A102-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A102-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A102-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000192 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000192/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A103-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A103-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A103-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000193 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000193/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A15V-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A15V-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A15V-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000194 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000194/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A15W-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A15W-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A15W-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000195 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000195/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A15X-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A15X-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A15X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000196 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000196/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A15Z-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A15Z-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A15Z-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000197 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000197/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A160-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A160-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A160-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000198 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000198/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A161-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A161-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A161-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000199 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000199/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A163-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A163-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A163-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000200 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000200/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A165-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A165-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A165-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000201 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000201/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A167-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A167-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A167-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000202 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000202/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A168-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A168-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A168-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000203 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000203/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A169-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A169-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A169-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000204 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000204/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16B-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16B-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000205 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000205/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16D-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16D-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000206 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000206/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16E-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16E-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16E-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000207 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000207/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16F-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16F-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000208 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000208/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16G-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16G-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16G-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000209 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000209/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16I-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16I-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16I-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000210 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000210/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16J-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16J-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16J-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000211 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000211/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16N-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16N-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000212 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000212/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16O-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16O-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16O-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000213 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000213/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16Q-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16Q-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000214 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000214/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16R-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16R-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000215 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000215/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16S-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16S-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000216 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000216/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16X-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16X-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16X-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000217 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000217/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A16Y-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A16Y-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A16Y-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000218 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000218/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A174-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A174-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A174-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000219 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000219/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A176-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A176-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A176-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000220 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000220/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A177-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A177-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A177-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000221 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000221/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17A-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17A-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17A-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000222 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000222/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17B-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17B-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17B-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000223 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000223/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17C-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17C-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17C-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000224 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000224/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17D-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17D-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17D-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000225 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000225/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17F-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17F-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17F-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000226 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000226/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17H-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17H-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17H-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000227 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000227/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17K-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17K-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17K-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000228 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000228/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17L-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17L-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17L-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000229 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000229/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17M-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17M-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17M-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000230 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000230/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17N-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17N-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17N-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000231 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000231/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17Q-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17Q-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17Q-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000232 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000232/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17R-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17R-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17R-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000233 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000233/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17S-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17S-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17S-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000234 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000234/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17T-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17T-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17T-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000235 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000235/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A17U-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A17U-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A17U-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000236 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000236/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A1NU-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A1NU-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A1NU-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000237 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000237/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-D1-A1NX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-D1-A1NX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-D1-A1NX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000238 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000238/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-DI-A0WH-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-DI-A0WH-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-DI-A0WH-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000239 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000239/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-DI-A1NN-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-DI-A1NN-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-DI-A1NN-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000240 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000240/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-E6-A1LZ-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-E6-A1LZ-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-E6-A1LZ-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000241 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000241/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-EO-A1Y5-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-EO-A1Y5-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-EO-A1Y5-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000242 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000242/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-EO-A1Y8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-EO-A1Y8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-EO-A1Y8-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000243 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000243/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-EY-A1GS-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-EY-A1GS-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-EY-A1GS-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000244 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000244/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-EY-A212-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-EY-A212-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-EY-A212-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000245 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000245/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-FI-A2D2-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-FI-A2D2-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-FI-A2D2-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000246 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000246/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-FI-A2EW-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-FI-A2EW-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-FI-A2EW-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000247 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000247/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-FI-A2EX-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-FI-A2EX-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-FI-A2EX-01.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000248 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216205/iteration1/scatter.0000000248/*; cd "/xchip/gdac_data" && cd "/xchip/cga1/annotation" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_216205   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar   "/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt" "/xchip/cga1/annotation/db/tracks/hg19/c65e/all.fwb" 1 845 "UCEC-FI-A2F8-TP" "hg19" "/xchip/cga1/annotation/db/ucsc/hg19" "UCEC-FI-A2F8-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/ucec/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.2.7.0/TCGA-FI-A2F8-01.wig.txt"

Finished submitting scatter jobs at Wed Oct 24 16:16:05 2012 in 3.15474323432 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_216205) -J gather_216205 -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/" "UCEC" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/UCEC/1911650/0.MutSigPreprocess.Finished/UCEC.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/UCEC/1911650/0.MutSigPreprocess.Finished/UCEC.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_216205) -J iteration_216205 -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 216205 --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
