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Unable to load library 'lsf': liblsf.so
I had no problem to run GATK two weeks ago. But today, when I run the following GATK command, I got error message. It seems it cannot load library " liblsf.so". Please see below. Is there any change recently on GATK library?
2:15pm [email protected] /bit/data01/projects/GC_coverage $ java -Xmx4g -Djava.io.tmpdir=/broad/hptmp/vdauwera -jar /humgen/gsa-scr1/vdauwera/gatk/walker/dist/Queue.jar -S /bit/data01/projects/GC_coverage/src/IntervalCovGG.scala -i /humgen/gsa-hpprojects/GATK/data/genes_of_interest.exon_targets.interval_list -b /bit/data01/projects/GC_coverage/testGCcoverage/data/DEV-2129.list -o /bit/data01/projects/GC_coverage/testGCcoverage/DEV-2129.gatkreport -m 16 -sc 100 -bsub -jobQueue priority -startFromScratch -run
The error shows:
ERROR 14:13:06,238 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.sting.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:9 0) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf 706JobRunner.scala:233) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.<clinit>(L sf706JobRunner.scala) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf7 06JobRunner.scala:47) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf 706JobManager.scala:35) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf 706JobManager.scala:33) at org.broadinstitute.sting.queue.engine.QGraph.newRunner(QGraph.scala:6 32) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:408 ) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:131) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scal a:127) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:146) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala: 62) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load librar y '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.sting.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:9 .........