SVPreprocess MergeInsertSizeHistograms error

ArtArt South San FranciscoMember


I'm getting an OutOfMemoryError heap space error running SVPreprocess on 50 BAMs (see attached log file). The error occurs with MergeInsertSizeHistograms, which, if I understand the following forum discussion correctly, shouldn't even run if I use reduceInsertSizeDistributions:

Up-adjusting memory doesn't solve the problem. I'm using v 2.00.1592, and the installtest runs fine. I've pasted my settings below.

I'd be very grateful for any advice on how to fix this.

Thank you for your help,


java -cp ${classpath} ${mx} \

org.broadinstitute.gatk.queue.QCommandLine \

-S ${SV_DIR}/qscript/SVPreprocess.q \

-S ${SV_DIR}/qscript/SVQScript.q \

-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \

--disableJobReport \

-cp ${classpath} \

-configFile ${dataDir}/genstrip_parameters.txt \

-tempDir ${SV_TMPDIR} \

-R ${dataDir}/GRCh38.fa \

-genomeMaskFile ${dataDir}/GRCh38.mask.100.fasta \

-copyNumberMaskFile ${dataDir}/GRCh38.cn2_mask.fasta \

-genderMapFile ${dataDir}/ \

-ploidyMapFile ${dataDir}/ \

-runDirectory ${runDir} \

-md ${runDir}/metadata \

-disableGATKTraversal \

-useMultiStep \

-reduceInsertSizeDistributions true \

-computeGCProfiles true \

-computeReadCounts true \

-jobLogDir ${runDir}/logs \

-I ${bam} \

-run \

-jobRunner Drmaa \

-gatkJobRunner Drmaa \

|| exit 1

Best Answer


  • ArtArt South San FranciscoMember

    Hi Seva, I just ran SVPreprocess with the parameters you suggested and it worked perfectly. Thank you!

  • Hi Art,

    Great, I am glad it worked!


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