Holiday Notice:
The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!

GenomeSTRIP CNVDiscoveryPipeline without LSF

a_ka_k Member
edited September 2016 in GenomeSTRiP


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
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 \
-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 \

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': cannot open shared object file: No such file or directory
at com.sun.jna.NativeLibrary.loadLibrary(
at com.sun.jna.NativeLibrary.getInstance(
at com.sun.jna.NativeLibrary.getInstance(
at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.(
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.QCommandLine.execute(QCommandLine.scala:170)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
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.

Best Answers


Sign In or Register to comment.