Queue with LSF v8.3?

wxingwxing Posts: 6Member

Hi,

I am testing queue scripts with new installed LSF v8.3. The test script is:

java -Djava.io.tmpdir=/tmp -jar jar2216/Queue.jar -S Queue-2.2-16-g9f648cb/resources/ExampleCountReads.scala -R Queue-2.2-16-g9f648cb/resources/exampleFASTA.fasta -I Queue-2.2-16-g9f648cb/resources/exampleBAM.bam --bsub -run

where I get error message as follows:

'java' '-Xmx1024m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/data/cmb/wxing/gatk/.queue/tmp' '-cp' '/data/cmb/wxing/gatk/jar2216/Queue.jar' 'org.broadinstitute.sting.gatk.
CommandLineGATK' '-T' 'CountReads' '-I' '/data/cmb/wxing/gatk/Queue-2.2-16-g9f648cb/resources/exampleBAM.bam' '-R' '/data/cmb/wxing/gatk/Queue-2.2-16-g9f648cb/resources/exampleFASTA.fasta'
java.lang.UnsatisfiedLinkError: Error looking up function 'ls_getLicenseUsage': /usr/local/lsf/8.3/linux2.6-glibc2.3-x86_64/lib/liblsf.so: undefined symbol: ls_getLicenseUsage
at com.sun.jna.Function.(Function.java:179)
at com.sun.jna.NativeLibrary.getFunction(NativeLibrary.java:344)
at com.sun.jna.NativeLibrary.getFunction(NativeLibrary.java:324)
at com.sun.jna.Native.register(Native.java:1341)
at com.sun.jna.Native.register(Native.java:1018)
at org.broadinstitute.sting.jna.lsf.v7_0_6.LibLsf.(LibLsf.java:86)
at java.lang.J9VMInternals.initializeImpl(Native Method)
at java.lang.J9VMInternals.initialize(J9VMInternals.java:200)
at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.unitDivisor(Lsf706JobRunner.scala:401)
at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.org$broadinstitute$sting$queue$engine$lsf$Lsf706JobRunner$$convertUnits(Lsf706JobRunner.scala:416)
at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner.start(Lsf706JobRunner.scala:98)
at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:83)
at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:432)
at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:154)
at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:145)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

Any clues on the issue "java.lang.UnsatisfiedLinkError: Error looking up function 'ls_getLicenseUsage': /usr/local/lsf/8.3/linux2.6-glibc2.3-x86_64/lib/liblsf.so: ". Or anyone had similar problems?

Anyone think it could be the version of our LSF (v8.3) as the code seem based on version 706?

Many thanks, Wei

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  • wxingwxing Posts: 6Member

    many many thanks! So I will comment the line in LibLSF.java and ant the new jar file. Thanks again, Wei

  • Mark_DePristoMark_DePristo Posts: 153Administrator, GATK Developer admin

    It would be very useful if you could do this against our git repository, and issue a patch to us, so we can easily incorporate the functionality in future GATK releases.

    --
    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

  • wxingwxing Posts: 6Member

    No problem. I will issue a patch to GATK git repo after I do QA tests (user cases) internally at ICR. Regards, Wei

  • wxingwxing Posts: 6Member

    hi, is that possible that I can have the GATK 2.0 source code or I can have a bugfix version of GATK Queue.jar?

    I have the source from github of GATK Lite, bug-fix to enable the LSF v8.x, re-compile to have a bugfix new Queue.jar. However, just realized that it does not include the RedeuceReader.class...

    Thanks, Wei

  • wxingwxing Posts: 6Member

    Many thanks! Wei

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