Re: [svtoolkit-help] SVPreprocess MergeInsertSizeHistograms error

[Bob H. <han...@br...>]

I corrected the information in that post.
That information was correct at the time, but has since changed (the old 
way caused problems if you tried to merge preprocessing directories with 
non-disjoint bams).
The memory footprint can be controlled if your bams are disjoint (use 
-bamFilesAreDisjoint true).
If they are not disjoint (i.e. you have the same samples/libraries/read 
groups in multiple input bam files), then the easiest solution is to 
give more memory to MergeInsertSizeHistograms.
Most bams are disjoint, but the default is to be conservative.

-Bob

On 6/15/15 11:07 PM, Arthur Wuster wrote:
> 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${runDir}/metadata \
>
> -disableGATKTraversal\
>
> -useMultiStep\
>
> -reduceInsertSizeDistributionstrue\
>
> -computeGCProfilestrue\
>
> -computeReadCountstrue\
>
> -jobLogDir${runDir}/logs \
>
> -I${bam}\
>
> -run\
>
> -jobRunnerDrmaa \
>
> -gatkJobRunnerDrmaa \
>
> -jobProjectsv_nov14 \
>
> -jobNative"-R rusage[mem=16]"-jobNative"-q long"\
>
> -jobQueuelong \
>
>     || exit1
>
>
>
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>
>
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