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Error when running UG: Unexpected base in allele bases

akiezunakiezun Cambridge, MAPosts: 22Member, Dev
edited August 2012 in Ask the GATK team

Hi,
I got the following error when running UG (on unstable from 2012/08/15, v2.0-222-gc178076)

java.lang.IllegalArgumentException: Unexpected base in allele bases 'T^@'
        at org.broadinstitute.sting.utils.variantcontext.Allele.<init>(Allele.java:115)
        at org.broadinstitute.sting.utils.variantcontext.Allele.create(Allele.java:167)
        at org.broadinstitute.sting.utils.variantcontext.Allele.create(Allele.java:272)
        at org.broadinstitute.sting.gatk.walkers.annotator.DepthPerAlleleBySample.annotateIndel(DepthPerAlleleBySample.java:91)
        at org.broadinstitute.sting.gatk.walkers.annotator.DepthPerAlleleBySample.annotate(DepthPerAlleleBySample.java:52)
        at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateGenotypes(VariantAnnotatorEngine.java:282)
        at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:201)
        at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateGenotypes(UnifiedGenotyperEngine.java:499)
        at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:192)
        at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:354)
        at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:119)
        at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:65)
        at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.0-222-gc178076):

The arguments were something like this (modified here for readability)
Program Args: -T UnifiedGenotyper -I My.bam.list -L scatter.intervals -R /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta -dcov 60 -glm BOTH -capMaxAltAllelesForIndels -D /humgen/gsa-pipeline/resources/b37/v4/dbsnp_135.b37.vcf -o My.unfiltered.vcf

I put the bams and actual logs etc on the local disk at the Broad:
/xchip/cga2/akiezun/forSharing/UnexpectedBaseErrorI

I also saw the same error (modulo the precise message) on many of my other UG runs that all use the same build 2.0-222-gc178076

Best Answer

Answers

  • ebanksebanks Broad InstitutePosts: 698Member, Administrator, Broadie, Moderator, Dev admin

    Thanks for reporting this Adam. It doesn't seem like this error should be possible with a well-formed bam, but I'd be happy to look into it. Unfortunately, I don't have read access to any of the bams in your bam list, so I'll need a little help from you. Can you please isolate the issue to small interval and then run PrintReads on that interval with your bam list, printing out to a location that I can read? I'll then take it from there.
    Thanks!

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • akiezunakiezun Cambridge, MAPosts: 22Member, Dev

    Thanks for your response. I just sent the small testcase by email.

    ./adam

  • bwubbbwubb Posts: 51Member

    Hi, just wanted to say I got a similar error trying to SomaticIndelCaller with GATK v2.1-5

    ##### ERROR stack trace 
    java.lang.IllegalArgumentException: Unexpected base in allele bases '65C'
        at org.broadinstitute.sting.utils.variantcontext.Allele.<init>(Allele.java:115)
        at org.broadinstitute.sting.utils.variantcontext.Allele.create(Allele.java:167)
        at org.broadinstitute.sting.utils.variantcontext.Allele.create(Allele.java:272)
        at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector.fillAlleleList(SomaticIndelDetector.java:1184)
        at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector.printVCFLine(SomaticIndelDetector.java:1232)
        at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector.emit_somatic(SomaticIndelDetector.java:979)
        at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector.map(SomaticIndelDetector.java:580)
        at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector.map(SomaticIndelDetector.java:131)
        at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:104)
        at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:52)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:71)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:265)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.1-5-gf3daab0):
    

    My bam was generated through v3 Best Practices, not sure if that is a contributing factor.

    Thank you

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