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A fatal error has been detected by the Java Runtime Environment while running Genome Strip.

SyedSyed IndiaMember
edited April 2016 in GenomeSTRiP

Hello Every one,

I was trying to run Genometsrip CNV discovery for one of sample and I am getting below error.

INFO 14:42:06,029 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/.queue/tmp' '-cp' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/lib/SVToolkit.jar:/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/lib/SVToolkit.jar:/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.discovery.SVDepthScanner' '-O' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/testCNV/cnv_stage1/seq_9/seq_9.sites.vcf.gz' '-R' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/reference_metadata_bundles/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta' '-genomeMaskFile' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/reference_metadata_bundles/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta' '-genomeMaskFile' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/reference_metadata_bundles/Homo_sapiens_assembly19/Homo_sapiens_assembly19.lcmask.fasta' '-genderMapFile' 'gender_map_file.txt' '-md' 'testCNV/metadata' '-configFile' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/conf/genstrip_parameters.txt' '-L' '9' '-tilingWindowSize' '1000' '-tilingWindowOverlap' '500' '-maximumReferenceGapLength' '1000'
INFO 14:42:06,030 FunctionEdge - Output written to /gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/testCNV/cnv_stage1/seq_9/logs/CNVDiscoveryStage1-1.out
#

A fatal error has been detected by the Java Runtime Environment:

#

SIGSEGV (0xb) at pc=0x00000037f8d32d5f, pid=26385, tid=47583501379328

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JRE version: Java(TM) SE Runtime Environment (8.0_66-b17) (build 1.8.0_66-b17)

Java VM: Java HotSpot(TM) 64-Bit Server VM (25.66-b17 mixed mode linux-amd64 compressed oops)

Problematic frame:

C [libc.so.6+0x132d5f]

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Core dump written. Default location: /gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/core or core.26385

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An error report file with more information is saved as:

/gpfs/projects/bioinfo/najeeb/CNV_pipeline/GenomeStrip/svtoolkit/hs_err_pid26385.log

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25,1 53%
I tried both Java 1.7 and Java 1.8 with Genomestrip 2.00 1650 and 2.00 1636 as well. While Preprocessing step is working but CNVDiscovery is giving errors. I am using LSF for submitting jobs as bsub -n 8 scripname.sh .
I am attaching script for kind pursual as well.

Someone please help me on this.

Post edited by Syed on

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