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CNV Discovery Stage 7 Error

jfarrelljfarrell Member ✭✭

The following error occurs during CNVDiscoveryStage7. Are there any suggestions or workarounds?

INFO  12:57:09,377 QCommandLine - Scripting CNVDiscoveryStage7
INFO  12:57:09,610 QCommandLine - Added 2 functions
INFO  12:57:09,611 QGraph - Generating graph.
INFO  12:57:09,623 QGraph - Running jobs.
INFO  12:57:10,396 FunctionEdge - Starting:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/restricted/projectnb/casa/sv/gs/.queue/tmp'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.discovery.MergeBrigVcfFiles'  '-R' '/restricted/projectnb/casa/sv/gs/svtoolkit/1000G_phase1/human_g1k_v37.fasta'  '-vcfFile' 'run.bcm/cnv_stage7/seq_GL000202.1/brig.vcf.file.list'  '-mergedVcfFile' 'run.bcm/cnv_stage7/seq_GL000202.1/seq_GL000202.1.brig.sites.vcf'
INFO  12:57:10,396 FunctionEdge - Output written to /restricted/projectnb/casa/sv/gs/run.bcm/cnv_stage7/seq_GL000202.1/logs/CNVDiscoveryStage7-1.out
INFO  12:57:10,576 DrmaaJobRunner - Submitted job id: 7358120
INFO  12:57:10,578 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done
ERROR 12:57:41,534 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/restricted/projectnb/casa/sv/gs/.queue/tmp'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.discovery.MergeBrigVcfFiles'  '-R' '/restricted/projectnb/casa/sv/gs/svtoolkit/1000G_phase1/human_g1k_v37.fasta'  '-vcfFile' 'run.bcm/cnv_stage7/seq_GL000202.1/brig.vcf.file.list'  '-mergedVcfFile' 'run.bcm/cnv_stage7/seq_GL000202.1/seq_GL000202.1.brig.sites.vcf'
ERROR 12:57:41,545 FunctionEdge - Contents of /restricted/projectnb/casa/sv/gs/run.bcm/cnv_stage7/seq_GL000202.1/logs/CNVDiscoveryStage7-1.out:
INFO  12:57:29,384 HelpFormatter - ---------------------------------------------------------------
INFO  12:57:29,387 HelpFormatter - Program Name: org.broadinstitute.sv.discovery.MergeBrigVcfFiles
INFO  12:57:29,393 HelpFormatter - Program Args: -R /restricted/projectnb/casa/sv/gs/svtoolkit/1000G_phase1/human_g1k_v37.fasta -vcfFile run.bcm/cnv_stage7/seq_GL000202.1/brig.vcf.file.list -mergedVcfFile run.bcm/cnv_stage7/seq_GL000202.1/seq_GL000202.1.brig.sites.vcf
INFO  12:57:29,396 HelpFormatter - Executing as [email protected] on Linux 2.6.32-504.3.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_21-b11.
INFO  12:57:29,397 HelpFormatter - Date/Time: 2015/04/09 12:57:29
INFO  12:57:29,397 HelpFormatter - ---------------------------------------------------------------
INFO  12:57:29,397 HelpFormatter - ---------------------------------------------------------------
Exception in thread "main" java.lang.RuntimeException
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:61)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
        at org.broadinstitute.sv.discovery.MergeBrigVcfFiles.main(MergeBrigVcfFiles.java:50)
Caused by: java.lang.NullPointerException
        at org.broadinstitute.sv.discovery.MergeBrigVcfFiles.updateVCFHeader(MergeBrigVcfFiles.java:112)
        at org.broadinstitute.sv.discovery.MergeBrigVcfFiles.mergeVCFFiles(MergeBrigVcfFiles.java:84)
        at org.broadinstitute.sv.discovery.MergeBrigVcfFiles.run(MergeBrigVcfFiles.java:56)
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50)
        ... 4 more
INFO  12:57:41,546 QGraph - Writing incremental jobs reports...
INFO  12:57:41,546 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done
INFO  12:57:41,548 QCommandLine - Writing final jobs report...
INFO  12:57:41,548 QCommandLine - Done with errors
INFO  12:57:41,550 QGraph - -------
INFO  12:57:41,551 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/restricted/projectnb/casa/sv/gs/.queue/tmp'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.discovery.MergeBrigVcfFiles'  '-R' '/restricted/projectnb/casa/sv/gs/svtoolkit/1000G_phase1/human_g1k_v37.fasta'  '-vcfFile' 'run.bcm/cnv_stage7/seq_GL000202.1/brig.vcf.file.list'  '-mergedVcfFile' 'run.bcm/cnv_stage7/seq_GL000202.1/seq_GL000202.1.brig.sites.vcf'
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Best Answer

Answers

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    Thanks for starting a new issue for this.
    Take a look at run.bcm/cnv_stage7/seq_GL000202.1/brig.vcf.file.list and share it (and maybe the files it points to) if you can.
    I have a guess, but let's see what the data looks like.

  • jfarrelljfarrell Member ✭✭

    To get around this, the cnv discovery was limited to chr1-22, X and Y by adding the -intervalList reference_chromosomes.list parameter.

    Unfortunately for debugging, those files above are not available at this point as it was run with -startFromScratch.

    I will try to get an example with another run.

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