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possible bug when running UnifiedGenotyper on Sanger reads

d17d17 Member
edited December 2012 in Ask the GATK team

Hi,

I am trying to run UnifiedGenotyper on ~20 samples sequenced to relatively low coverage (~1-4X) with Sanger reads in yeast. The UG starts out running fine, getting through the first two chromosomes with no problem. Then I get the following error:

##### ERROR stack trace 
java.lang.IllegalArgumentException: 628 > 398
    at java.util.Arrays.copyOfRange(Arrays.java:3064)
    at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeGeneralReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:353)
    at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeDiploidReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:197)
    at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getLikelihoods(IndelGenotypeLikelihoodsCalculationModel.java:127)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:285)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:190)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:346)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:121)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23)
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
    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)

The arguments I am specifying to GATK are:

 -T UnifiedGenotyper -baq RECALCULATE -glm BOTH -stand_call_conf 20.0 -stand_emit_conf 20.0

and of course I specify -I for each of my bam files and the reference with -R.

Any ideas what might be going wrong? Or ideas for how I could narrow down what the problem might be?
For what it's worth, I am using GATK v2.2-8-gec077cd.

Answers

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