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SVPreprocess MergeInsertSizeHistograms error

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:
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
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skashin ✭✭
Hi Art,
In the post you make a reference to there is a correction saying that now one needs to specify both reduceInsertSizeDistributions true and -bamFilesAreDisjoint true to skip this step.
So if all your bam files contain separate libraries add -bamFilesAreDisjoint true to your script.
And you might want to download and use Genome STRiP Release 2.00.1599, and drop the argument “-useMultiStep"
Seva
Answers
Hi Art,
In the post you make a reference to there is a correction saying that now one needs to specify both reduceInsertSizeDistributions true and -bamFilesAreDisjoint true to skip this step.
So if all your bam files contain separate libraries add -bamFilesAreDisjoint true to your script.
And you might want to download and use Genome STRiP Release 2.00.1599, and drop the argument “-useMultiStep"
Seva
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!
Seva