Error when running UG: Unexpected base in allele bases
Posted in Ask the team | Last updated on 2012-08-19 01:43:22


Comments (4)

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


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