Dear all
We have run into a problem while running CNVDiscovery. The errors are occurring during Stage 7. An example of the type of error can be seen below:
ERROR 00:13:56,742 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCT\ imeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/lcottino/attempt8/ALL/.queue/tmp' '-cp' '/opt/exp_soft/bio\ inf/svtoolkit/lib/SVToolkit.jar:/opt/exp_soft/bioinf/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/opt/exp_soft/bioinf/svtoolkit\ /lib/gatk/Queue.jar' '-cp' '/opt/exp_soft/bioinf/svtoolkit/lib/SVToolkit.jar:/opt/exp_soft/bioinf/svtoolkit/lib/gatk/Genom\ eAnalysisTK.jar:/opt/exp_soft/bioinf/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.genotyping.RefineCNVBoundaries' \ '-I' '/home/lcottino/attempt8/ALL/Run1/cnv_stage6/seq_7/seq_7.merged_headers.bam' '-O' '/home/lcottino/attempt8/ALL/Run1/\ cnv_stage7/seq_7/P0134/seq_7.merged.brig.vcf' '-R' '/home/lcottino/references/Homo_sapiens_assembly19/Homo_sapiens_assembl\ y19.fasta' '-md' '/home/lcottino/attempt8/ALL/output_metadata_directory' '-configFile' '/opt/exp_soft/bioinf/svtoolkit/co\ nf/genstrip_parameters.txt' '-P' 'depth.readCountCacheIgnoreGenomeMask:true' '-genomeMaskFile' '/home/lcottino/references\ /Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta' '-genomeMaskFile' '/home/lcottino/references/Homo_sapiens_as\ sembly19/Homo_sapiens_assembly19.lcmask.fasta' '-genderMapFile' '/home/lcottino/attempt8/genderMaps/gender.map' '-ploidyM\ apFile' '/home/lcottino/references/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt' '-vcf' 'Run1/cnv_stage4/\ seq_7/seq_7.merged.genotypes.vcf.gz' '-site' 'Run1/cnv_stage7/seq_7/P0134.sites.list' '-boundaryPrecision' '100' '-minim\ umRefinedLength' '500' '-maximumReferenceGapLength' '1000' ERROR 00:13:56,781 FunctionEdge - Contents of /home/lcottino/attempt8/ALL/Run1/cnv_stage7/seq_7/logs/CNVDiscoveryStage7-135\ .out:
However, the VCF output is produced and looks good and when we check the CNVDiscoveryStage7-135 log it says that it is done without errors. Furthermore, if we run it manually there is no problem.
We have tried to rerun it to see if it will correct itself but the same error occurred.
Stage 7 also seems to overwhelm the cluster, with 1000s of jobs being submitted - is this supposed to be happening?
We'd be very grateful for any advice on trying to work out where the problem is.
Kind regards,
Laura