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Haplotypecaller and stack trace error

weesedaweeseda University of MichiganMember

I'm having trouble running the haplotypecaller on a few of my samples. Before I go full scale on all of my samples I am attempting the pipeline on a small number of my samples. When I try running haplotypecaller on my samples individually with the command below I get a stack trace error (also below). Usually I can figure out the stack trace errors and correct them, but I am having trouble with this one. With this error, the program runs for a time then errors out (sometime it runs longer then other times). It doesn't occur for every sample and when it does occur, if I re-run that same individual and same command again it sometimes goes to completion without errors. Other times I might have to run that individual/command multiple times before I can get it to complete without errors. Any insight would be greatly appreciated.

java -Xmx16g -jar ~/programs/GenomeAnalysisTK.jar -T HaplotypeCaller -R ../miliaris_ref.fa -I realigned/27861_realigned.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 --max_alternate_alleles 2 -mbq 30 -recoverDanglingHeads -dontUseSoftClippedBases -stand_call_conf 4.0 -stand_emit_conf 3.0 -o rawSNPS_Q4/27861_rawSNPS_Q4.vcf -nct 8 -A HaplotypeScore -A FisherStrand -A BaseQualityRankSumTest -A MappingQualityRankSumTest -A ReadPosRankSumTest -A QualByDepth -A VariantType -A LowMQ

INFO 12:36:15,578 ProgressMeter - comp45464_c0_seq1:533 2.82e+06 2.5 m 53.0 s 7.1% 35.2 m 32.7 m
INFO 12:36:45,579 ProgressMeter - comp45609_c0_seq1:269 2.84e+06 3.0 m 63.0 s 7.2% 41.9 m 38.9 m
INFO 12:37:15,580 ProgressMeter - comp48164_c0_seq1:493 3.09e+06 3.5 m 67.0 s 7.8% 44.9 m 41.4 m
WARN 12:37:24,038 ExactAFCalc - this tool is currently set to genotype at most 2 alternate alleles in a given context, but the context at comp48440_c0_seq1:357 has 6 alter$
INFO 12:37:45,581 ProgressMeter - comp53167_c0_seq2:450 3.67e+06 4.0 m 65.0 s 9.2% 43.3 m 39.3 m

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

at java.lang.String.checkBounds(
at java.lang.String.(
at net.sf.samtools.util.StringUtil.bytesToString(
at net.sf.samtools.BAMRecord.decodeReadName(
at net.sf.samtools.BAMRecord.getReadName(
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph.addRead(
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.createGraph(
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.assemble(
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LocalAssemblyEngine.runLocalAssembly(
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.assembleReads(
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$
at java.util.concurrent.Executors$
at java.util.concurrent.FutureTask$Sync.innerRun(
at java.util.concurrent.ThreadPoolExecutor.runWorker(
at java.util.concurrent.ThreadPoolExecutor$

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    Can you tell me two things:

    1. What version of java are you using?

    2. Does the error still occur if you run without -nct?

  • weesedaweeseda University of MichiganMember

    Yes, I'm using the latest version; 3.1-1 and so far 2 samples have made it through w/o errors running without -nct. Testing more, but the que on our server is backed up so its taking awhile

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ok, let me know if you run into any issues without -nct. Some platforms just don't support it well.

    For the version I meant what version of Java, not GATK, because we've seen some people have problems after upgrading to Java 1.8. Currently GATK only supports Java 1.7.

  • weesedaweeseda University of MichiganMember

    Sorry, missed that. I'm running java version 1.7; haven't upgraded to 1.8 yet. Might take a bit longer, but I guess I'll just proceed w/o -nct for now.

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