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Stage 7 of CNVDiscoveryPipeline - all commands fail with java.lang.NullPointerException

d_a_parryd_a_parry EdinburghMember

I am attempting to run GenomeSTRiP's CNVDiscoveryPipeline. I have run SVPreprocess successfully and am now running CNVDiscoveryPipeline on a single chromosome. Each command at stage 7 fails with the following stack trace:

Exception in thread "main" java.lang.RuntimeException
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
    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.runAndReturnResult(CommandLineProgram.java:29)
    at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
    at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:133)
Caused by: java.lang.NullPointerException
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.computeNextCoordinate(BoundaryRefinementAlgorithm.java:886)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.getRefinedInterval(BoundaryRefinementAlgorithm.java:704)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:612)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:548)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:536)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:232)
    at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:204)
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
    ... 5 more

An example command for this stage is:

'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10' \
-Djava.io.tmpdir=/exports/eddie/scratch/dparry/bams/.queue/tmp'  \
'-cp' '/exports/igmm/eddie/aitman-lab/svtoolkit/lib/SVToolkit.jar:/exports/igmm/eddie/aitman-lab/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/exports/igmm/eddie/aitman-lab/svtoolkit/lib/gatk/Queue.jar' \
'-cp' '/exports/igmm/eddie/aitman-lab/svtoolkit/lib/SVToolkit.jar:/exports/igmm/eddie/aitman-lab/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/exports/igmm/eddie/aitman-lab/svtoolkit/lib/gatk/Queue.jar' \
'org.broadinstitute.sv.genotyping.RefineCNVBoundaries' \
'-I' '/exports/eddie/scratch/dparry/sids_bams/per_chrom/cnv_discovery_chr22/cnv_stage6/seq_chr22/seq_chr22.merged_headers.bam' \
'-O' '/exports/eddie/scratch/dparry/sids_bams/per_chrom/cnv_discovery_chr22/cnv_stage7/seq_chr22/P0354/seq_chr22.merged.brig.vcf' \
'-R' '/exports/igmm/software/pkg/el7/apps/bcbio/share2/genomes/Hsapiens/hg38-noalt/seq/hg38-noalt.fa' \
'-md' 'sv_meta_data'  \
'-configFile' '/exports/igmm/eddie/aitman-lab/svtoolkit/conf/genstrip_parameters.txt' \
'-P' 'depth.readCountCacheIgnoreGenomeMask:true'  \
'-genderMapFile' 'sv_meta_data/sample_gender.report.txt'  \
'-ploidyMapFile' '/exports/igmm/eddie/aitman-lab/svtoolkit/Homo_sapiens_assembly38/Homo_sapiens_assembly38.ploidymap.txt'  \
'-vcf' 'per_chrom/cnv_discovery_chr22/cnv_stage4/seq_chr22/seq_chr22.merged.genotypes.vcf.gz' \
'-site' 'per_chrom/cnv_discovery_chr22/cnv_stage7/seq_chr22/P0354.sites.list'  \
'-boundaryPrecision' '100' \
'-minimumRefinedLength' '500'  \
'-maximumReferenceGapLength' '1000'         

I have tested this on a different chromosome and get the same error. Any help figuring out what is going wrong would be much appreciated!

Thanks

Dave

Answers

  • nmkeurnmkeur NetherlandsMember
    edited December 2016
    
    Exception in thread "main" java.lang.RuntimeException
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
        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.runAndReturnResult(CommandLineProgram.java:29)
        at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
        at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:133)
    Caused by: java.lang.NullPointerException
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.computeNextCoordinate(BoundaryRefinementAlgorithm.java:886)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.getRefinedInterval(BoundaryRefinementAlgorithm.java:704)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:612)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:548)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:536)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:232)
        at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:204)
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
        ... 5 more 
    

    I am having the exact same problem as above. The pipeline seems to fail on stage7.
    I really appreciate any help you can provide.

    Thanks

    Nick

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