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Mutect2 error java.lang.NumberFormatException: For input string: "."

Hello, everyone
I'm trying to call snv using mutect2, gatk4.0.9.0 . And the bam was generated from gatk-bqsr.While many sample successfully finished the mutect2, some got ERROR MESSAGE:

INFO Mutect2 - Shutting down engine
[October 24, 2018 12:29:00 PM CST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 113.02 minutes.
Runtime.totalMemory()=4760535040
** java.lang.NumberFormatException: For input string: "."**
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at java.lang.Double.valueOf(Double.java:502)
at htsjdk.variant.variantcontext.CommonInfo.lambda$getAttributeAsDoubleList$2(CommonInfo.java:299)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Collections$2.tryAdvance(Collections.java:4717)
at java.util.Collections$2.forEachRemaining(Collections.java:4725)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsList(CommonInfo.java:273)
at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsDoubleList(CommonInfo.java:293)
at htsjdk.variant.variantcontext.VariantContext.getAttributeAsDoubleList(VariantContext.java:740)
at org.broadinstitute.hellbender.tools.walkers.mutect.GermlineProbabilityCalculator.getGermlineAltAlleleFrequencies(GermlineProbabilityCalculator.java:49)
at org.broadinstitute.hellbender.tools.walkers.mutect.GermlineProbabilityCalculator.getPopulationAFAnnotation(GermlineProbabilityCalculator.java:27)
at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.callMutations(SomaticGenotypingEngine.java:151)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.callRegion(Mutect2Engine.java:217)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.apply(Mutect2.java:215)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:291)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

Tagged:

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited October 2018

    Hi @youpingLi

    Would you please do a BAM file diagnosis by running ValidateSamFile . Please post the results of that here so we can figure out what the issue maybe here. Also you can follow this link for more information on fixing BAM related issue.

    Regards
    Bhanu

  • youpingLiyoupingLi Member
    edited October 2018

    Hello, @bhanuGandham Thanks for your reply.
    The ValidateSamFile result of bam include one ERROR:
    ERROR: Record 250717557, Read name SRR6359395.137294991, NM tag (nucleotide differences) in file [1] does not match reality [0]

    However, I have tried to use SetNmMdAndUqTags to fix our bam file.And ValidateSamFile result of fixed bam is :
    Runtime.totalMemory()=12957253632
    Tool returned:
    0

    But this didn't work.Mutect2 still came out with this same error.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited November 2018

    Hi @youpingLi

    Sorry for the delayed response. I will have the developers look into this and get back to you on Monday. Also it would be very helpful if you could post the exact command you are using. Thank you.

    Regards
    Bhanu

    Post edited by bhanuGandham on
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @youpingLi

    This is a bug that we are working on and you can follow the issue here. For a workaround please follow this thread.
    Hope this helps.

    Regards
    Bhanu

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