svGenotyper Error: Null Pointer

dantakidantaki La JollaMember

SVpreprocess seemed to run without error for my samples. However I'm getting an error with svGenotyper

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.NullPointerException
        at org.broadinstitute.sv.metadata.MetaData.computeSampleDoubleMap(MetaData.java:447)
        at org.broadinstitute.sv.metadata.MetaData.getSampleFragmentsPerBaseMap(MetaData.java:421)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.init(GenotypingDepthModule.java:1798)
        at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.initModules(GenotypingAlgorithm.java:522)
        at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.initialize(GenotypingAlgorithm.java:87)
        at org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:217)
        at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
        at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
        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.main.SVCommandLine.main(SVCommandLine.java:78)
        at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------
ERROR 15:17:09,789 FunctionEdge - Error:  'java'  '-Xmx4096m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/home/dantakli/bin/svtoolkit/cookbook/genotyping/1000G_phase1_local/.queue/tmp'  '-cp' '/home/dantakli/bin/svtoolkit/lib/SVToolkit.jar:/home/dantakli/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/dantakli/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVGenotyper '-T' 'SVGenotyperWalker'  '-R' '/oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/human_g1k_hs37d5.fasta'  '-I' '1kg_high_coverage_bam.list'  '-O' '/home/dantakli/bin/svtoolkit/cookbook/genotyping/1000G_phase1_local/1kg_highcov/P0006.genotypes.vcf.gz'  '-disableGATKTraversal' 'true'  '-md' '/oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata'  '-configFile' '/home/dantakli/bin/svtoolkit/conf/genstrip_parameters.txt'  '-runDirectory' '1kg_highcov'  '-genderMapFile' '/oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/1kg_p3_highcov_genderMapFile.list'  '-ploidyMapFile' '/oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/human_g1k_hs37d5.ploidymap.txt'  '-genomeMaskFile' '/oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/human_g1k_hs37d5.svmask.fasta'  '-vcf' '1kg_highcov_cnv_p3_calls.vcf'  '-partitionName' 'P0006'  '-partition' 'records:1501-1800'
ERROR 15:17:09,790 FunctionEdge - Contents of /home/dantakli/bin/svtoolkit/cookbook/genotyping/1000G_phase1_local/1kg_highcov/logs/SVGenotyper-6.out:

I have the correct metadata files and locations. Not sure why it crashed.

Answers

  • skashinskashin Member ✭✭

    Something seems to be wrong with your metadata directory. Are you sure SVPreprocess completed successfully, and if so, does the -md argument in SVGenotyper point to the right metadata directory? Is there depth.dat file in the metadata directory?

  • dantakidantaki La JollaMember

    I'm not sure if SVPreprocess completed or not. I get this error in the log files

    ERROR 19:36:27,139 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/home/dantakli/bin/svtoolkit/cookbook/genotyping/1000G_phase1_local/.queue/tmp'  '-cp' '/home/dantakli/bin/svtoolkit/lib/SVToolkit.jar:/home/dantakli/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/dantakli/bin/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/home/dantakli/bin/svtoolkit/lib/SVToolkit.jar:/home/dantakli/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/dantakli/bin/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms'  '-I' '/oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/isd/HG00096.wgs.ILLUMINA.bwa.GBR.high_cov_pcr_free.20140203.hist.bin'  '-O' '/oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/isd/HG00096.wgs.ILLUMINA.bwa.GBR.high_cov_pcr_free.20140203.dist.bin'
    ERROR 19:36:27,147 FunctionEdge - Contents of /oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/logs/SVPreprocess-36.out:
    

    But this is the last log file in the working directory (log file 65)

    INFO  05:56:25,705 HelpFormatter - -------------------------------------------------------------------
    INFO  05:56:25,707 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms
    INFO  05:56:25,710 HelpFormatter - Program Args: -I /oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/isd/NA20845.wgs.ILLUMINA.bwa.GIH.high_cov_pcr_free.20140203.hist.bin -O /oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/isd/NA20845.wgs.ILLUMINA.bwa.GIH.high_cov_pcr_free.20140203.dist.bin
    INFO  05:56:25,716 HelpFormatter - Executing as [email protected] on Linux 3.10.73-1.el6.elrepo.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_75-mockbuild_2015_01_20_23_39-b00.
    INFO  05:56:25,716 HelpFormatter - Date/Time: 2015/09/22 05:56:25
    INFO  05:56:25,716 HelpFormatter - -------------------------------------------------------------------
    INFO  05:56:25,716 HelpFormatter - -------------------------------------------------------------------
    Processing NA20845/Solexa-206023/null ...
    INFO  05:56:33,135 CommandLineProgram - Program completed.
    
  • skashinskashin Member ✭✭

    Sorry, I am a bit confused - what is in the log file /oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/logs/SVPreprocess-36.out?

  • dantakidantaki La JollaMember
    INFO  14:15:17,626 HelpFormatter - -------------------------------------------------------------------
    INFO  14:15:17,628 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms
    INFO  14:15:17,632 HelpFormatter - Program Args: -I /oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/isd/HG00759.wgs.ILLUMINA.bwa.CDX.high_cov_pcr_free.20140203.hist.bin -O /oasis/scratch/comet/dantakli/temp_project/1kg_p3_metadata/isd/HG00759.wgs.ILLUMINA.bwa.CDX.high_cov_pcr_free.20140203.dist.bin
    INFO  14:15:17,638 HelpFormatter - Executing as [email protected] on Linux 3.10.73-1.el6.elrepo.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_75-mockbuild_2015_01_20_23_39-b00.
    INFO  14:15:17,638 HelpFormatter - Date/Time: 2015/09/23 14:15:17
    INFO  14:15:17,638 HelpFormatter - -------------------------------------------------------------------
    INFO  14:15:17,638 HelpFormatter - -------------------------------------------------------------------
    Processing HG00759/Solexa-206019/null ...
    INFO  14:15:24,311 CommandLineProgram - Program completed.
    

    logs/SVPreprocess-36.out (END)

    There's no ERROR message

  • skashinskashin Member ✭✭

    Yes, it seems the program completed successfully, but it’s difficult for me to tell what’s going on as I can see 4 very different timestamps in the log file snippets you provided. Did you run the top-level pre-processing script more than once?
    If you do run it again and send the output to an empty file it will be easier to see what jobs failed and why. And when you run the script again, Queue will only rerun the jobs that previously failed

  • dantakidantaki La JollaMember

    Thanks for the help. I'm running it now and I'll see what happens. Good that it picks up from where it starts. wew

  • Did you resolve this issue? If so, what was the solution?

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