GenotypeGVCFs calculateLikelihoodSums NullPointerException

WimSWimS Member
edited July 2017 in Ask the GATK team

Hi,

I run into a NullPointerException exception when trying do use GenotypeGVCFs to merge a set of gVCF files stored via GenomicsDBImport in a database.

java.lang.NullPointerException
        at org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils.calculateLikelihoodSums(AlleleSubsettingUtils.java:234)
        at org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils.calculateMostLikelyAlleles(AlleleSubsettingUtils.java:199)
        at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:241)
        at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:205)
        at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.calculateGenotypes(GenotypeGVCFs.java:276)
        at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:234)
        at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:213)
        at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:110)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
        at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
        at java.util.Iterator.forEachRemaining(Iterator.java:116)
        at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
        at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:108)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:838)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:115)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:170)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:189)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:131)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:152)
        at org.broadinstitute.hellbender.Main.main(Main.java:230)

A pull request concerning a NullPointerException during GenotypeGVCFs calculateLikelihoodSums has been merged after the GATK4 beta1 release:
15 days ago
https://github.com/broadinstitute/gatk/pull/3212

22 days ago:
https://github.com/broadinstitute/gatk/releases/tag/4.beta.1

Can I somewhere download a GATK4 jar that contains the fix for the nullpointer issue in GenotypeGVCFs? ie,. a nightly build?

Thank you.

Post edited by WimS on

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