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Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Queue with LSF v8.3?

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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Best Answers

Answers

  • wxingwxing Posts: 6

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

  • Mark_DePristoMark_DePristo Broad InstitutePosts: 153 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: 6

    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: 6

    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: 6

    Many thanks! Wei

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