Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.