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

Question

[always_learning]

Hi,

I was trying to run Genome Strip but some how its not working. I tried to posted at Broad Institute Forum but it didn't work as well as no one even responded their.

http://gatkforums.broadinstitute.org/gatk/discussion/7381/a-fatal-error-has-been-detected-by-the-java-runtime-environment-while-running-genome-strip#latest

If some one else tried to run GenomeStrio and faced some problem then please help me on this.

Thanks

[QVINTVS_FABIVS_MAXIMVS]

Mahraban. Could you give more detail. Like if it's a memory issue? What does the log file say? GS has always given me troubles and the guys at Broad (shoutout to Bob) are really friendly. In the end I didn't use GS because it kept crashing and had to move on to other projects. Also just wondering, are you running CNV discovery after you generate all the metadata? I left a tad confused on your GATK link.

[always_learning]

yes I am able to generate metadata properly. And then I am getting this error at CNV discovery stage. I think this is something to do with LSF DRMAA configuration but since I am using DRMAA for preprocessing step as well but that step is successfully completed as well.

INFO 11:34:56,516 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/.queue/tmp' '-cp' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit//lib/SVToolkit.jar:/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit//lib/gatk/GenomeAnalysisTK.jar:/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit//lib/gatk/Queue.jar' '-cp' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/lib/SVToolkit.jar:/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.discovery.SVDepthScanner' '-O' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/testCNV/cnv_stage1/seq_18/seq_18.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' 'input_metadata_directory' '-configFile' '/gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/conf/genstrip_parameters.txt' '-L' '18' '-tilingWindowSize' '1000' '-tilingWindowOverlap' '500' '-maximumReferenceGapLength' '1000' INFO 11:34:56,517 FunctionEdge - Output written to /gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/testCNV/cnv_stage1/seq_18/logs/CNVDiscoveryStage1-1.out

A fatal error has been detected by the Java Runtime Environment: SIGSEGV (0xb) at pc=0x00000035de932d5f, pid=9197, tid=47497786693376 JRE version: 7.0_09 Java VM: OpenJDK 64-Bit Server VM (23.2-b09 mixed mode linux-amd64 compressed oops) Problematic frame: C [libc.so.6+0x132d5f] __tls_get_addr@@GLIBC_2.3+0x132d5f Core dump written. Default location: /gpfs/projects/bioinfo/najeeb/CNV_pipeline/svtoolkit/core or core.9197

[always_learning]

this is similar problem at forum. http://gatkforums.broadinstitute.org/gatk/discussion/5657/cnvdiscoverypipeline-nullpointerexception-lsf-8-drmaa-sigsegv

[always_learning]

this is similar problem at forum. http://gatkforums.broadinstitute.org/gatk/discussion/5657/cnvdiscoverypipeline-nullpointerexception-lsf-8-drmaa-sigsegv

Answer 1

[always_learning]

Its seems like issue with DRMAA config with LSF on our cluster.