GenomeSTRIP CNVDiscoveryPipeline without LSF

a_k · September 2016

Hello,

I am running GenomeSTRIP CNVDiscoveryPipeline on a set of bam files on a server that does not have LSF installed. Is there a separate mode that works on a standalone server, or is LSF a strict requirement regardless?

I am running the command
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
java -Xmx8g -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 \
-ploidyMapFile $PLOIDY_MAP_FILE \
-genderMapFile $GENDER_MAP_FILE \
-R $REFERENCE_GENOME \
-I $bam \
-md $OUTPUT_FOLDER/metadata \
-runDirectory $OUTPUT_FOLDER/run/$bam_id \
-jobLogDir $LOG_FOLDER \
-tilingWindowSize 1000 \
-tilingWindowOverlap 500 \
-maximumReferenceGapLength 1000 \
-boundaryPrecision 100 \
-minimumRefinedLength 500 \
-run

Unfortunately, I am not getting any calls in the output folder. Instead, I am seeing the following exception thrown in each log out file (such as CNVDiscoveryPipeline-304.out):

INFO 17:43:35,051 QCommandLine - Done with errors
Exception in thread "main" 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.(LibBat.java:91)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.(Lsf706JobRunner.scala:237)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.(Lsf706JobRunner.scala)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.(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:705)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:455)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
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)
INFO 17:43:35,055 QCommandLine - Shutting down jobs. Please wait...

How can I fix this issue and get CNV calls output?
Thanks for any help!

EDIT: Should probably be in GenomeSTRIP forum section.

Sheila · October 2016

@a_k
Hi,

Yes, I moved your question to the GenomeSTRiP category where @bhandsaker will help you.

-Sheila

bhandsaker · October 2016

In practice, you need to have some kind of cluster computing environment to be able to run Genome STRiP successfully. The methods are population-based, requiring many input samples, so you generally need at least 50-100 samples to process together to get best results. Doing this on a single machine is generally not tractable. I'm a little surprised you were able to get through GS preprocessing without hitting this problem already.

That being said, technically you can try with the arguments -jobRunner Shell -gatkJobRunner Shell. This will run single-threaded on the local host. There is also a ParallelShell option in Queue (use ParallelShell instead of Shell), but I haven't personally tried it.

Sheila · October 2016