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