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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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a fatal error by java runtime environement

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' '-Djava.io.tmpdir=/medpop/mpg-psrl/Parabase/tmp' '-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 [libjvm.so+0x712380] 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: > # http://java.sun.com/webapps/bugreport/crash.jsp > # >
the log file is lengthy; but If you like to have a look I can paste here it later on,
thanks for your support,
Tagged:
Answers
I'm not certain, but I think I see errors like this when LSF kills my job (for, e.g., exceeding wall time)
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.
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!
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.
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
java.lang.NegativeArraySizeException
at org.broadinstitute.sting.utils.SWPairwiseAlignment.align(SWPairwiseAlignment.java:95)
at org.broadinstitute.sting.utils.SWPairwiseAlignment.(SWPairwiseAlignment.java:79)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.addHaplotype(SimpleDeBruijnAssembler.java:335)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.findBestPaths(SimpleDeBruijnAssembler.java:293)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.runLocalAssembly(SimpleDeBruijnAssembler.java:69)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:394)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:107)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:285)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:230)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:205)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:131)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:28)
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:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
ERROR
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------
Thanks for any help!
Julia
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?