Unable to load library 'lsf': liblsf.so
Posted in Ask the GATK team | Last updated on 2013-01-15 20:02:25


Comments (6)

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 qyu@vbronze /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
.........

Thanks, Qing


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