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a fatal error by java runtime environement

naarkhoonaarkhoo Member Posts: 38
edited January 2013 in Ask the GATK team

I am facing a "fatal error by java runtime enviormnet" after using GATK DataProcessingPipeline,
my java version is

> java version "1.6.0_35"
> Java(TM) SE Runtime Environment (build 1.6.0_35-b10)
> Java HotSpot(TM) 64-Bit Server VM (build 20.10-b01, mixed mode)

and I am using GATK 2.3-6-gebbba25
The pipeline spit out the following error,

> lelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  ''  '-cp' '/medpop/mpg-psrl/Parabase/Tools/Queue-2.3-5-g49ed93c/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'RealignerTargetCreator'  '-I' '/medpop/mpg-psrl/Parabase/MyRuns/EX_c1004CARa_1ln_hg19._new.1.realigned.rg.bam'  '-R' '/medpop/mpg-psrl/Parabase/hg19/ucsc.hg19.fasta'  '-o' '/medpop/mpg-psrl/Parabase/MyRuns/EX_c1004CARa_1ln_hg19.EX_c1004CARa_1ln_hg19.intervals'  '-known' '/medpop/mpg-psrl/Parabase/hg19/dbsnp_137.hg19.vcf'  '-mismatch' '0.0'  
> INFO  11:32:30,896 FunctionEdge - Output written to /medpop/mpg-psrl/Parabase/MyRuns/EX_c1004CARa_1ln_hg19.EX_c1004CARa_1ln_hg19.intervals.out 
> #
> # A fatal error has been detected by the Java Runtime Environment:
> #
> #  SIGSEGV (0xb) at pc=0x00002ae7a5a50380, pid=562, tid=47174397446800
> #
> # JRE version: 6.0_35-b10
> # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.10-b01 mixed mode linux-amd64 compressed oops)
> # Problematic frame:
> # V  []  SR_handler(int, siginfo*, ucontext*)+0x30
> #
> # An error report file with more information is saved as:
> # /medpop/mpg-psrl/Parabase/MyRuns/hs_err_pid562.log
> #
> # If you would like to submit a bug report, please visit:
> #
> #

the log file is lengthy; but If you like to have a look I can paste here it later on,
thanks for your support,


  • pdexheimerpdexheimer Member, Dev Posts: 544 ✭✭✭✭

    I'm not certain, but I think I see errors like this when LSF kills my job (for, e.g., exceeding wall time)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin

    Yes, that looks like a problem in your server setup. Unfortunately that's not something we can help you with; I recommend you get support from your IT department to sort this out.

    Geraldine Van der Auwera, PhD

  • JulsJuls Graz, AustriaMember Posts: 18

    Dear Geraldine_VdAuwera: I also get this error message when running the HaplotypeCaller. Everything else worked fine. What do you mean by a problem in your server setup? Could you be a bit more specific? Thank you very much!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin

    Hi @Juls,

    It's difficult to say, as this type of error is not directly related to GATK. You should consult your IT department about this, they will be able to help you much better than us.

    Geraldine Van der Auwera, PhD

  • JulsJuls Graz, AustriaMember Posts: 18

    Hi @Geraldine_VdAuwera,

    Thank you for your answer!
    I've now upgraded java to the latest version, as this was suggested elsewhere for SIGSEGV errors. Now I get the following error (It occurs when executing the HaplotypeCaller) and I don't think this is a server setup problem (not that I know that much about java .. :)

    INFO 16:54:27,828 ProgressMeter - S01_GL985056:2293760 2.28e+06 5.2 h 2.3 h 6.9% 76.3 h 71.0 h
    INFO 16:55:27,846 ProgressMeter - S01_GL985056:2392064 2.38e+06 5.2 h 2.2 h 7.2% 73.4 h 68.1 h
    INFO 16:56:27,868 ProgressMeter - S01_GL985056:2392064 2.38e+06 5.3 h 2.2 h 7.2% 73.6 h 68.3 h
    INFO 16:57:12,468 GATKRunReport - Uploaded run statistics report to AWS S3

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

    at org.broadinstitute.sting.utils.SWPairwiseAlignment.align(
    at org.broadinstitute.sting.utils.SWPairwiseAlignment.(
    at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.addHaplotype(
    at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.findBestPaths(
    at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.runLocalAssembly(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
    ERROR Please visit the wiki to see if this is a known problem
    ERROR If not, please post the error, with stack trace, to the GATK forum
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions
    ERROR MESSAGE: Code exception (see stack trace for error itself)
    ERROR ------------------------------------------------------------------------------------------

    Thanks for any help!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin

    Ah, this is more our domain, yes :)

    This looks like a bug that was fixed in a more recent version -- can you update your GATK version to 2.6 and try again?

    Geraldine Van der Auwera, PhD

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