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