Error in VariantEval
Posted in Ask the team | Last updated on 2012-08-14 01:32:37


Comments (9)

Hi, I'm running 1.6-512-gafa4399 (unstable).

When running VariantEval, I got an error: "Couldn't find state for 88 at node org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratNode"

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Couldn't find state for 88 at node org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratNode@1a7df60a
at org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratNode.find(StratNode.java:117)
at org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager.getKeys(StratificationManager.java:208)
at org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager.values(StratificationManager.java:260)
at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker.getEvaluationContexts(VariantEvalWalker.java:480)
at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker.map(VariantEvalWalker.java:406)
at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker.map(VariantEvalWalker.java:89)
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:63)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:257)
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:92)

This happened on running VariantEval like this:

-T VariantEval -L /xchip/cga/reference/hg19/whole_exome_agilent_1.1_refseq_plus_3_boosters_plus_10bp_padding_minus_mito.Homo_sapiens_assembly19.targets.interval_list -R /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta -nt 1 -o myFile.byAC.eval -eval myFile.vcf -D dbsnp_132_b37.leftAligned.vcf -gold /humgen/gsa-hpprojects/GATK/bundle/current/b37/Mills_and_1000G_gold_standard.indels.b37.sites.vcf -ST EvalRod -ST CompRod -ST Novelty -ST FunctionalClass -ST AlleleCount -noST -EV TiTvVariantEvaluator -EV CountVariants -EV CompOverlap -EV IndelSummary -noEV 

Do you know what may be causing this error? If it helps, I can distill a small failing vcf. ./adam


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