FilterMutectCalls Error: java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN

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Jared Jurss

• February 27, 2020 18:13

I am running GATK version 4.1.4.1

The command used is:

gatk FilterMutectCalls  -R human_ref_GRCh38_all_alt.fa -V test.vcf.gz  -O filtered.vcf.gz

Error:

java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN
at org.broadinstitute.hellbender.utils.NaturalLogUtils.logSumExp(NaturalLogUtils.java:84)
at org.broadinstitute.hellbender.utils.NaturalLogUtils.normalizeLog(NaturalLogUtils.java:51)
at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.clusterProbabilities(SomaticClusteringModel.java:203)
at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.learnAndClearAccumulatedData(SomaticClusteringModel.java:122)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.learnParameters(Mutect2FilteringEngine.java:156)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.afterNthPass(FilterMutectCalls.java:159)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)

The VCF file being used was generated using GATK's best practices for data pre-processing and GATK's best practice workflow for Somatic short variant discovery.

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  Tiffany Miller

  • March 02, 2020 17:37

  Hello Jared Jurss ,

  Another user reported this bug with 4.1.4.0 and David introduced some changes that should hopefully fix this. Can you try using the latest version, 4.1.5.0, and let us know if you still see it?

   

   

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  Jared Jurss

  • March 05, 2020 22:38

  Hey Tiffany,

  I updated my version of GATK as you suggested and FilterMutectCalls seems to be working now.  Thank you!

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  Tiffany Miller

  • March 06, 2020 16:49

  Awesome! No problem!

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