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Using Genome STRiP with SLURM instead of LSF

ryanfriedman22ryanfriedman22 Washington University in St. LouisMember
edited July 2016 in GenomeSTRiP

I'm trying to use the most recent release of Genome STRiP for CNV calling, but my cluster doesn't use LSF. As a result, I'm getting following error all over the place:
ERROR 17:15:10,412 QGraph - Uncaught error running jobs. java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34) at org.broadinstitute.gatk.queue.engine.QGraph.newRunner(QGraph.scala:715) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:457) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:157) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:170) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

We use SLURM on our cluster. I saw on a previous post something about DRMAA support, which SLURM does. Are there additional options I can provide to make this run? Below is what I'm currently running. I have to cd into SV_DIR, otherwise I get errors of a queue system file not being found because SV_DIR is getting left out of the path for some reason:

strains=$1
runDir=$2
workDir=pwd
SV_DIR="/scratch/mblab/ryan.friedman/svtoolkit/"
cd ${SV_DIR}
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

java -Xmx20g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R ${SV_DIR}/crNeoH99/crNeoH99.fasta \
-I ${workDir}/${strains} \
-genderMapFile ${SV_DIR}/crNeoH99/crNeoH99.gendermask.bed \
-md ${SV_DIR}/crNeoH99/ \
-runDirectory ${workDir}/${runDir} \
-jobLogDir ${workDir}/${runDir}/logs \
-tilingWindowSize 1000 \
-tilingWindowOverlap 500 \
-maximumReferenceGapLength 1000 \
-boundaryPrecision 100 \
-minimumRefinedLength 500 \
-run

Answers

  • cwhelancwhelan Cambridge, MAMember, Broadie, Dev

    I'm not sure what the right parameters for SLURM are but to use DRMAA you'll want to add something like:

    -jobRunner Drmaa \
    -gatkJobRunner Drmaa \
    -jobNative ' XX ' \
    -jobNative ' YY ' \

    where XX and YY are different options to pass to the SLURM job submitter.

    Hope that helps.

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