We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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}/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


  • 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!


Sign In or Register to comment.