SVPreprocess MergeInsertSizeHistograms error
Art
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:
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
-
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