Re: [svtoolkit-help] Error reported without any debugging info - can ignore?
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Re: [svtoolkit-help] Error reported without any debugging info - can ignore?
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From: Bob H. <han...@br...> - 2013-12-20 17:47:57
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That is odd - I don't have any easy explanation. And I haven't seen this or gotten any similar reports. Are you using a clean run directory (as opposed to trying to use the run directory already used by another run, like installtest)? You need to use a clean run directory for every run (and also in most cases if you change the input parameters). Are you running through LSF, SGE or some other load manager or just running serially (i.e. without -bsub)? It seems like somehow Queue is seeing a non-zero exit status from the process, even though it completed successfully. Did Queue create an .<output-file>.done sentinel file for these two output (e.g. metadata/.depth.dat.done) ? Is there a metadata/.depth.dat.fail ? -Bob On 12/20/13 12:13 PM, Noll, Aaron wrote: > > Hello, > > I am trying to use genomeStrip to identify known CNVs in a simulated > dataset. > > I have had success with the installTest so believe that svtoolkit is > properly installed/configured. > > When running the preprocess steps on my bam file I see an Error for > the 8^th step but no further information is provided. As you can see > the log file for that step only has "INFO" lines. > > This also occurs for the 9^th step. (pasted farther down) > > When I attempt to run these steps individually after getting these > errors there is no sign of any issues. > > I turned on the jobReports option but the output wasn't helpful. > > Any ideas on how to debug this, should I ignore these errors? > > Thanks, > > Aaron > > INFO 08:49:52,546 QGraph - 3 Pend, 2 Run, 0 Fail, 7 Done > > ERROR 08:49:52,558 FunctionEdge - Error: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.MergeReadDepthCoverage' '-I' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/depth/sampleC_7723_del_40.align.sorted.depth.txt' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/depth.dat' > > ERROR 08:49:52,563 FunctionEdge - Contents of > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-8.out: > > INFO 08:16:16,570 HelpFormatter - > --------------------------------------------------------------- > > INFO 08:16:16,572 HelpFormatter - Program Name: > org.broadinstitute.sv.apps.MergeReadDepthCoverage > > INFO 08:16:16,576 HelpFormatter - Program Args: -I > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/depth/sampleC_7723_del_40.align.sorted.depth.txt > -O > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/depth.dat > > INFO 08:16:16,576 HelpFormatter - Date/Time: 2013/12/20 08:16:16 > > INFO 08:16:16,577 HelpFormatter - > --------------------------------------------------------------- > > INFO 08:16:16,577 HelpFormatter - > --------------------------------------------------------------- > > INFO 08:16:16,585 CommandLineProgram - Program completed. > > INFO 08:49:52,571 FunctionEdge - Done: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > org.broadinstitute.sv.main.SVCommandLine '-T' > 'ComputeReadSpanCoverageWalker' '-R' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/data/human_b36_chr1.fasta' > '-I' > '/home/anoll/sim/readSim/wgsim/sampleC_7723_del_40.align.sorted.bam' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans/sampleC_7723_del_40.align.sorted.spans.txt' > '-disableGATKTraversal' 'true' '-md' 'test1/metadata' > '-maxInsertSizeStandardDeviations' '3' > > INFO 08:49:52,571 QGraph - Writing incremental jobs reports... > > INFO 08:49:52,574 FunctionEdge - Starting: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans/sampleC_7723_del_40.align.sorted.spans.txt' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans.dat' > > INFO 08:49:52,575 FunctionEdge - Output written to > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-10.out > > INFO 08:49:57,940 FunctionEdge - Starting: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > org.broadinstitute.sv.main.SVCommandLine '-T' > 'ComputeGCProfileWalker' '-R' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/data/human_b36_chr1.fasta' > '-I' > '/home/anoll/sim/readSim/wgsim/sampleC_7723_del_40.align.sorted.bam' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/gcprofile/sampleC_7723_del_40.align.sorted.bam.gcprof.zip' > '-disableGATKTraversal' 'true' '-md' 'test1/metadata' > '-referenceProfile' 'test1/metadata/gcprofile/reference.gcprof.zip' > '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' > '-copyNumberMaskFile' 'data/cn2_mask_g1k_b36_chr1.fasta' > '-insertSizeRadius' '10.0' > > INFO 08:49:57,940 FunctionEdge - Output written to > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-11.out > > INFO 09:14:22,959 QGraph - 1 Pend, 2 Run, 1 Fail, 8 Done > > INFO 08:16:16,598 FunctionEdge - Output written to > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-9.out > > INFO 08:49:52,546 QGraph - 3 Pend, 2 Run, 0 Fail, 7 Done > > ERROR 08:49:52,558 FunctionEdge - Error: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.MergeReadDepthCoverage' '-I' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/depth/sampleC_7723_del_40.align.sorted.depth.txt' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/depth.dat' > > ERROR 08:49:52,563 FunctionEdge - Contents of > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-8.out: > > INFO 08:16:16,570 HelpFormatter - > --------------------------------------------------------------- > > INFO 08:16:16,572 HelpFormatter - Program Name: > org.broadinstitute.sv.apps.MergeReadDepthCoverage > > INFO 08:16:16,576 HelpFormatter - Program Args: -I > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/depth/sampleC_7723_del_40.align.sorted.depth.txt > -O > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/depth.dat > > INFO 08:16:16,576 HelpFormatter - Date/Time: 2013/12/20 08:16:16 > > INFO 08:16:16,577 HelpFormatter - > --------------------------------------------------------------- > > INFO 08:16:16,577 HelpFormatter - > --------------------------------------------------------------- > > INFO 08:16:16,585 CommandLineProgram - Program completed. > > INFO 08:49:52,571 FunctionEdge - Done: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > org.broadinstitute.sv.main.SVCommandLine '-T' > 'ComputeReadSpanCoverageWalker' '-R' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/data/human_b36_chr1.fasta' > '-I' > '/home/anoll/sim/readSim/wgsim/sampleC_7723_del_40.align.sorted.bam' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans/sampleC_7723_del_40.align.sorted.spans.txt' > '-disableGATKTraversal' 'true' '-md' 'test1/metadata' > '-maxInsertSizeStandardDeviations' '3' > > INFO 08:49:52,571 QGraph - Writing incremental jobs reports... > > INFO 08:49:52,574 FunctionEdge - Starting: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans/sampleC_7723_del_40.align.sorted.spans.txt' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans.dat' > > INFO 08:49:52,575 FunctionEdge - Output written to > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-10.out > > INFO 08:49:57,940 FunctionEdge - Starting: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > org.broadinstitute.sv.main.SVCommandLine '-T' > 'ComputeGCProfileWalker' '-R' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/data/human_b36_chr1.fasta' > '-I' > '/home/anoll/sim/readSim/wgsim/sampleC_7723_del_40.align.sorted.bam' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/gcprofile/sampleC_7723_del_40.align.sorted.bam.gcprof.zip' > '-disableGATKTraversal' 'true' '-md' 'test1/metadata' > '-referenceProfile' 'test1/metadata/gcprofile/reference.gcprof.zip' > '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' > '-copyNumberMaskFile' 'data/cn2_mask_g1k_b36_chr1.fasta' > '-insertSizeRadius' '10.0' > > INFO 08:49:57,940 FunctionEdge - Output written to > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-11.out > > INFO 09:14:22,959 QGraph - 1 Pend, 2 Run, 1 Fail, 8 Done > > ERROR 09:14:22,971 FunctionEdge - Error: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans/sampleC_7723_del_40.align.sorted.spans.txt' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans.dat' > > ERROR 09:14:22,973 FunctionEdge - Contents of > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-10.out: > > INFO 08:49:57,915 HelpFormatter - > -------------------------------------------------------------- > > INFO 08:49:57,917 HelpFormatter - Program Name: > org.broadinstitute.sv.apps.MergeReadSpanCoverage > > INFO 08:49:57,920 HelpFormatter - Program Args: -I > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans/sampleC_7723_del_40.align.sorted.spans.txt > -O > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/spans.dat > > INFO 08:49:57,921 HelpFormatter - Date/Time: 2013/12/20 08:49:57 > > INFO 08:49:57,921 HelpFormatter - > -------------------------------------------------------------- > > INFO 08:49:57,921 HelpFormatter - > -------------------------------------------------------------- > > INFO 08:49:57,927 CommandLineProgram - Program completed. > > INFO 09:14:22,987 FunctionEdge - Done: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > org.broadinstitute.sv.main.SVCommandLine '-T' > 'ComputeGCProfileWalker' '-R' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/data/human_b36_chr1.fasta' > '-I' > '/home/anoll/sim/readSim/wgsim/sampleC_7723_del_40.align.sorted.bam' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/gcprofile/sampleC_7723_del_40.align.sorted.bam.gcprof.zip' > '-disableGATKTraversal' 'true' '-md' 'test1/metadata' > '-referenceProfile' 'test1/metadata/gcprofile/reference.gcprof.zip' > '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' > '-copyNumberMaskFile' 'data/cn2_mask_g1k_b36_chr1.fasta' > '-insertSizeRadius' '10.0' > > INFO 09:14:22,988 QGraph - Writing incremental jobs reports... > > INFO 09:14:22,991 FunctionEdge - Starting: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.MergeGCProfiles' '-I' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/gcprofile/sampleC_7723_del_40.align.sorted.bam.gcprof.zip' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/gcprofiles.zip' > > INFO 09:14:22,991 FunctionEdge - Output written to > /home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/logs/SVPreprocess-12.out > > INFO 09:14:28,331 QGraph - 0 Pend, 1 Run, 2 Fail, 9 Done > > INFO 09:14:52,970 FunctionEdge - Done: 'java' '-Xmx4096m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/tmpdir' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/SVToolkit.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.MergeGCProfiles' '-I' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/gcprofile/sampleC_7723_del_40.align.sorted.bam.gcprof.zip' > '-O' > '/home/anoll/tools/CNV/genome/doc/genomeStrip/svtoolkit/installtest/test1/metadata/gcprofiles.zip' > > INFO 09:14:52,971 QGraph - Writing incremental jobs reports... > > INFO 09:14:52,972 QGraph - 0 Pend, 0 Run, 2 Fail, 10 Done > > INFO 09:14:52,974 QCommandLine - Writing final jobs report... > > > ------------------------------------------------------------------------ > Electronic mail from Children's Mercy Hospitals and Clinics. 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