To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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

Best Answer

Answers

Sign In or Register to comment.