I am running CNVDiscoveryPipeline and it is throwing following error Unable to load library 'lsf': liblsf.so.
The command used is
java -Xmx150g -cp ${classpath} org.broadinstitute.gatk.queue.QCommandLine -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q -S ${SV_DIR}/qscript/SVQScript.q -cp ${classpath} -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar -maximumReferenceGapLength 1000 -md test3_complete/preprocess -minimumRefinedLength 500 -R genomic.fasta -runDirectory test3/cnvdiscovery -tilingWindowOverlap 500 -tilingWindowSize 1000 -boundaryPrecision 100 -I sorted.bam -intervalList reference_chromosomes.list -run
_The error encountered is _
INFO 20:29:04,367 HelpFormatter - Executing as on Linux 3.13.0-79-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_72-internal-b15.
INFO 20:29:04,367 HelpFormatter - Date/Time: 2018/02/19 20:29:04
INFO 20:29:04,368 HelpFormatter - ----------------------------------------------------------------------
INFO 20:29:04,368 HelpFormatter - ----------------------------------------------------------------------
INFO 20:29:04,374 QCommandLine - Scripting CNVDiscoveryStage1
INFO 20:29:04,425 QCommandLine - Added 2 functions
INFO 20:29:04,425 QGraph - Generating graph.
INFO 20:29:04,435 QGraph - Running jobs.
ERROR 20:29:04,484 QGraph - Uncaught error running jobs.
java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory
at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.(LibBat.java:91)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.(Lsf706JobRunner.scala:237)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.(Lsf706JobRunner.scala)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.(Lsf706JobRunner.scala:48)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34)
at org.broadinstitute.gatk.queue.engine.QGraph.org$broadinstitute$gatk$queue$engine$QGraph$$newRunner(QGraph.scala:925)
at org.broadinstitute.gatk.queue.engine.QGraph.startOneJob(QGraph.scala:643)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:507)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:168)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:170)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
INFO 20:29:04,487 QCommandLine - Done with errors
Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory
at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.(LibBat.java:91)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.(Lsf706JobRunner.scala:237)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.(Lsf706JobRunner.scala)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.(Lsf706JobRunner.scala:48)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34)
at org.broadinstitute.gatk.queue.engine.QGraph.org$broadinstitute$gatk$queue$engine$QGraph$$newRunner(QGraph.scala:925)
at org.broadinstitute.gatk.queue.engine.QGraph.startOneJob(QGraph.scala:643)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:507)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:168)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:170)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
INFO 20:29:04,491 QCommandLine - Shutting down jobs. Please wait...
I tried with parameters --gatkJobRunner Drmaa -jobRunner Drmaa also but it is throwing error "Unable to load library 'drmaa': libdrmaa.so".
Please help me installing the libraries.
Thanks
Juhi