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SVPreprocess MergeInsertSizeHistograms error

ArtArt South San FranciscoMember

Hi,

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:

http://gatkforums.broadinstitute.org/discussion/2167/genomestrip-svpreprocess-q-java-heap-space-error

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,

Art

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}/oct14_sex.map \

-ploidyMapFile ${dataDir}/humgen_g1k_v38_ploidy.map \

-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

Answers

  • ArtArt South San FranciscoMember

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

  • skashinskashin Member ✭✭

    Hi Art,

    Great, I am glad it worked!

    Seva

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