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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,