calling:  bsub -r -R select[tmp>1000 && scratch>1] -q cga -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/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.50.3134/prepare.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48863/LAML.coverage.prepare.txt /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48863/LAML.patients.txt /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48863/LAML.maf
Started submitting scatter jobs at Mon Dec  5 23:55:37 2011
calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000001 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000001/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2802" "LAML-AB-2802.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2802-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000002 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000002/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2803" "LAML-AB-2803.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2803-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000003 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000003/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2804" "LAML-AB-2804.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2804-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000004 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000004/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2805" "LAML-AB-2805.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2805-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000005 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000005/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2806" "LAML-AB-2806.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2806-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000006 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000006/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2807" "LAML-AB-2807.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2807-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000007 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000007/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2808" "LAML-AB-2808.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2808-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000008 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000008/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2809" "LAML-AB-2809.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2809-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000009 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000009/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2810" "LAML-AB-2810.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2810-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000010 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000010/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2811" "LAML-AB-2811.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2811-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000011 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000011/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2812" "LAML-AB-2812.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2812-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000012 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000012/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2813" "LAML-AB-2813.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2813-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000013 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000013/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2814" "LAML-AB-2814.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2814-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000014 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000014/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2815" "LAML-AB-2815.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2815-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000015 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000015/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2816" "LAML-AB-2816.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2816-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000016 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000016/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2817" "LAML-AB-2817.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2817-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000017 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000017/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2818" "LAML-AB-2818.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2818-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000018 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000018/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2819" "LAML-AB-2819.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2819-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000019 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000019/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2820" "LAML-AB-2820.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2820-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000020 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000020/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2821" "LAML-AB-2821.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2821-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000021 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000021/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2822" "LAML-AB-2822.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2822-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000022 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000022/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2823" "LAML-AB-2823.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2823-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000023 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000023/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2824" "LAML-AB-2824.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2824-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000024 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000024/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2825" "LAML-AB-2825.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2825-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000025 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000025/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2826" "LAML-AB-2826.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2826-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000026 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000026/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2827" "LAML-AB-2827.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2827-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000027 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000027/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2828" "LAML-AB-2828.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2828-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000028 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000028/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2829" "LAML-AB-2829.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2829-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000029 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000029/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2830" "LAML-AB-2830.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2830-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000030 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000030/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2831" "LAML-AB-2831.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2831-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000031 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000031/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2832" "LAML-AB-2832.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2832-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000032 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000032/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2833" "LAML-AB-2833.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2833-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000033 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000033/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2834" "LAML-AB-2834.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2834-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000034 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000034/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2835" "LAML-AB-2835.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2835-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000035 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000035/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2836" "LAML-AB-2836.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2836-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000036 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000036/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2837" "LAML-AB-2837.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2837-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000037 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000037/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2838" "LAML-AB-2838.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2838-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000038 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000038/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2839" "LAML-AB-2839.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2839-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000039 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000039/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2840" "LAML-AB-2840.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2840-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000040 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000040/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2841" "LAML-AB-2841.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2841-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000041 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000041/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2842" "LAML-AB-2842.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2842-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000042 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000042/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2843" "LAML-AB-2843.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2843-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000043 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000043/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2844" "LAML-AB-2844.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2844-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000044 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000044/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2845" "LAML-AB-2845.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2845-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000045 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000045/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2846" "LAML-AB-2846.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2846-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000046 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000046/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2847" "LAML-AB-2847.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2847-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000047 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000047/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2848" "LAML-AB-2848.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2848-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000048 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000048/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2849" "LAML-AB-2849.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2849-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000049 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000049/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2850" "LAML-AB-2850.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2850-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000050 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000050/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2851" "LAML-AB-2851.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2851-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000051 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000051/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2853" "LAML-AB-2853.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2853-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000052 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000052/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2854" "LAML-AB-2854.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2854-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000053 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000053/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2855" "LAML-AB-2855.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2855-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000054 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000054/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2856" "LAML-AB-2856.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2856-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000055 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000055/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2857" "LAML-AB-2857.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2857-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000056 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000056/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2858" "LAML-AB-2858.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2858-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000057 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000057/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2859" "LAML-AB-2859.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2859-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000058 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000058/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2860" "LAML-AB-2860.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2860-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000059 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000059/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2861" "LAML-AB-2861.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2861-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000060 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000060/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2862" "LAML-AB-2862.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2862-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000061 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000061/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2863" "LAML-AB-2863.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2863-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000062 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000062/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2864" "LAML-AB-2864.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2864-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000063 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000063/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2865" "LAML-AB-2865.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2865-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000064 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000064/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2866" "LAML-AB-2866.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2866-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000065 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000065/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2867" "LAML-AB-2867.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2867-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000066 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000066/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2868" "LAML-AB-2868.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2868-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000067 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000067/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2869" "LAML-AB-2869.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2869-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000068 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000068/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2870" "LAML-AB-2870.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2870-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000069 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000069/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2871" "LAML-AB-2871.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2871-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000070 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000070/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2872" "LAML-AB-2872.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2872-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000071 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000071/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2873" "LAML-AB-2873.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2873-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000072 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000072/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2874" "LAML-AB-2874.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2874-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000073 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000073/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2875" "LAML-AB-2875.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2875-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000074 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000074/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2876" "LAML-AB-2876.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2876-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000075 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000075/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2877" "LAML-AB-2877.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2877-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000076 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000076/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2878" "LAML-AB-2878.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2878-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000077 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000077/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2879" "LAML-AB-2879.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2879-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000078 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000078/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2880" "LAML-AB-2880.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2880-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000079 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000079/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2881" "LAML-AB-2881.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2881-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000080 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000080/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2882" "LAML-AB-2882.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2882-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000081 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000081/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2883" "LAML-AB-2883.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2883-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000082 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000082/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2884" "LAML-AB-2884.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2884-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000083 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000083/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2885" "LAML-AB-2885.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2885-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000084 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000084/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2886" "LAML-AB-2886.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2886-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000085 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000085/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2887" "LAML-AB-2887.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2887-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000086 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000086/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2888" "LAML-AB-2888.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2888-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000087 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000087/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2889" "LAML-AB-2889.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2889-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000088 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000088/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2890" "LAML-AB-2890.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2890-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000089 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000089/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2891" "LAML-AB-2891.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2891-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000090 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000090/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2892" "LAML-AB-2892.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2892-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000091 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000091/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2893" "LAML-AB-2893.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2893-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000092 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000092/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2894" "LAML-AB-2894.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2894-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000093 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000093/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2895" "LAML-AB-2895.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2895-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000094 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000094/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2896" "LAML-AB-2896.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2896-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000095 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000095/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2897" "LAML-AB-2897.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2897-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000096 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000096/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2898" "LAML-AB-2898.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2898-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000097 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000097/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2899" "LAML-AB-2899.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2899-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000098 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000098/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2900" "LAML-AB-2900.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2900-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000099 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000099/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2901" "LAML-AB-2901.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2901-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000100 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000100/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2903" "LAML-AB-2903.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2903-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000101 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000101/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2904" "LAML-AB-2904.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2904-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000102 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000102/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2905" "LAML-AB-2905.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2905-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000103 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000103/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2906" "LAML-AB-2906.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2906-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000104 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000104/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2907" "LAML-AB-2907.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2907-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000105 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000105/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2908" "LAML-AB-2908.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2908-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000106 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000106/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2909" "LAML-AB-2909.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2909-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000107 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000107/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2910" "LAML-AB-2910.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2910-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000108 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000108/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2911" "LAML-AB-2911.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2911-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000109 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000109/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2912" "LAML-AB-2912.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2912-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000110 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000110/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2913" "LAML-AB-2913.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2913-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000111 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000111/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2914" "LAML-AB-2914.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2914-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000112 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000112/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2915" "LAML-AB-2915.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2915-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000113 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000113/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2916" "LAML-AB-2916.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2916-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000114 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000114/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2917" "LAML-AB-2917.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2917-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000115 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000115/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2918" "LAML-AB-2918.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2918-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000116 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000116/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2919" "LAML-AB-2919.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2919-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000117 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000117/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2920" "LAML-AB-2920.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2920-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000118 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000118/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2921" "LAML-AB-2921.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2921-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000119 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000119/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2922" "LAML-AB-2922.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2922-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000120 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000120/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2923" "LAML-AB-2923.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2923-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000121 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000121/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2924" "LAML-AB-2924.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2924-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000122 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000122/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2925" "LAML-AB-2925.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2925-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000123 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000123/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2926" "LAML-AB-2926.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2926-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000124 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000124/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2927" "LAML-AB-2927.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2927-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000125 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000125/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2928" "LAML-AB-2928.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2928-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000126 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000126/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2929" "LAML-AB-2929.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2929-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000127 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000127/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2930" "LAML-AB-2930.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2930-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000128 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000128/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2931" "LAML-AB-2931.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2931-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000129 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000129/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2932" "LAML-AB-2932.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2932-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000130 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000130/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2933" "LAML-AB-2933.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2933-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000131 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000131/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2934" "LAML-AB-2934.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2934-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000132 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000132/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2935" "LAML-AB-2935.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2935-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000133 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000133/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2936" "LAML-AB-2936.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2936-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000134 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000134/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2937" "LAML-AB-2937.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2937-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000135 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000135/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2938" "LAML-AB-2938.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2938-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000136 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000136/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2939" "LAML-AB-2939.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2939-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000137 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000137/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2940" "LAML-AB-2940.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2940-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000138 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000138/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2941" "LAML-AB-2941.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2941-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000139 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000139/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2942" "LAML-AB-2942.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2942-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000140 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000140/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2943" "LAML-AB-2943.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2943-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000141 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000141/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2944" "LAML-AB-2944.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2944-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000142 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000142/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2945" "LAML-AB-2945.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2945-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000143 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000143/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2946" "LAML-AB-2946.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2946-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000144 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000144/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2947" "LAML-AB-2947.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2947-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000145 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000145/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2948" "LAML-AB-2948.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2948-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000146 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000146/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2949" "LAML-AB-2949.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2949-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000147 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000147/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2950" "LAML-AB-2950.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2950-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000148 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000148/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2952" "LAML-AB-2952.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2952-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000149 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000149/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2954" "LAML-AB-2954.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2954-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000150 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000150/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2955" "LAML-AB-2955.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2955-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000151 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000151/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2956" "LAML-AB-2956.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2956-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000152 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000152/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2957" "LAML-AB-2957.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2957-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000153 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000153/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2959" "LAML-AB-2959.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2959-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000154 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000154/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2963" "LAML-AB-2963.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2963-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000155 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000155/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2964" "LAML-AB-2964.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2964-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000156 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000156/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2965" "LAML-AB-2965.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2965-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000157 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000157/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2966" "LAML-AB-2966.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2966-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000158 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000158/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2967" "LAML-AB-2967.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2967-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000159 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000159/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2968" "LAML-AB-2968.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2968-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000160 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000160/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2969" "LAML-AB-2969.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2969-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000161 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000161/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2970" "LAML-AB-2970.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2970-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000162 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000162/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2971" "LAML-AB-2971.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2971-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000163 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000163/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2972" "LAML-AB-2972.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2972-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000164 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000164/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2973" "LAML-AB-2973.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2973-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000165 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000165/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2974" "LAML-AB-2974.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2974-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000166 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000166/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2976" "LAML-AB-2976.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2976-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000167 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000167/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2977" "LAML-AB-2977.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2977-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000168 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000168/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2978" "LAML-AB-2978.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2978-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000169 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000169/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2979" "LAML-AB-2979.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2979-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000170 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000170/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2980" "LAML-AB-2980.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2980-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000171 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000171/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2981" "LAML-AB-2981.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2981-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000172 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000172/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2982" "LAML-AB-2982.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2982-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000173 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000173/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2983" "LAML-AB-2983.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2983-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000174 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000174/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2984" "LAML-AB-2984.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2984-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000175 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000175/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2985" "LAML-AB-2985.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2985-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000176 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000176/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2986" "LAML-AB-2986.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2986-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000177 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000177/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2987" "LAML-AB-2987.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2987-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000178 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000178/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2988" "LAML-AB-2988.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2988-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000179 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000179/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2989" "LAML-AB-2989.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2989-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000180 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000180/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2990" "LAML-AB-2990.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2990-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000181 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000181/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2991" "LAML-AB-2991.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2991-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000182 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000182/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2992" "LAML-AB-2992.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2992-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000183 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000183/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2993" "LAML-AB-2993.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2993-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000184 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000184/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2994" "LAML-AB-2994.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2994-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000185 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000185/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2995" "LAML-AB-2995.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2995-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000186 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000186/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2996" "LAML-AB-2996.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2996-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000187 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000187/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2997" "LAML-AB-2997.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2997-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000188 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000188/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2998" "LAML-AB-2998.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2998-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000189 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000189/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2999" "LAML-AB-2999.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-2999-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000190 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000190/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3000" "LAML-AB-3000.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3000-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000191 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000191/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3001" "LAML-AB-3001.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3001-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000192 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000192/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3002" "LAML-AB-3002.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3002-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000193 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000193/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3005" "LAML-AB-3005.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3005-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000194 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000194/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3006" "LAML-AB-3006.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3006-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000195 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000195/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3007" "LAML-AB-3007.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3007-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000196 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000196/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3008" "LAML-AB-3008.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3008-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000197 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000197/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3009" "LAML-AB-3009.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3009-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000198 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000198/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3011" "LAML-AB-3011.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3011-03.wig.txt"

calling:  bsub -r -R rusage[mem=7] -R select[tmp>1000 && scratch>1] -q cga -P Firehose -sp 65 -cwd /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000199 -E rm -rf /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48864/iteration1/scatter.0000000199/*; cd "/xchip/gdac_data" && cd "/xchip/cga1" && cd "/xchip/tcga" && cd "/xchip/cga" -Q EXCLUDE(167) -e scatter.err -o scatter.out -J scatter_48864   java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ExtractFromWigAllChr.jar   "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3012" "LAML-AB-3012.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AB-3012-03.wig.txt"

Finished submitting scatter jobs at Mon Dec  5 23:57:17 2011 in 1.66984761556 minutes
calling:  bsub -E cd "/xchip/cga1" && 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_48864) -J gather_48864 -P Firehose -R rusage[mem=7] -sp 65   python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/run_matlab.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/ fh_MutSigCoverageGather   "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/" "LAML" "/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48863/LAML.maf" "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65" "4" "/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/48863/LAML.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_48864) -J iteration_48864 -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 48864 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.50.3134/
Path iteration1 exists:  True
