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,