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java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so

alirezakjalirezakj Member
edited March 2015 in GenomeSTRiP

Hi Bob,

While running CNV discovery with the command below:

java -cp ${classpath} ${mx} \ 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 \ -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ -R data/human_g1k_v37.fasta \ -I ${bamList} \ -genderMapFile data/geneder1000GandMysamples.map \ -md ${runDir}/metadata \ -runDirectory ${runDir} \ -intervalList 1 \ -jobLogDir ${runDir}/logs \ -tilingWindowSize 5000 \ -tilingWindowOverlap 2500 \ -maximumReferenceGapLength 2500 \ -boundaryPrecision 200 \ -minimumRefinedLength 2500 \ -run

I ran into an error saying:

ERROR 20:42:28,301 FunctionEdge - Contents of /media/WD4TB3/svtoolkit/MyRunDir/JAK3project/logs/CNVDiscoveryPipeline-3.out: INFO 20:42:03,789 QScriptManager - Compiling 4 QScripts INFO 20:42:15,331 QScriptManager - Compilation complete INFO 20:42:15,476 HelpFormatter - ---------------------------------------------------------------------- INFO 20:42:15,476 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/02/06 10:59:46 INFO 20:42:15,477 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 20:42:15,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 20:42:15,477 HelpFormatter - Program Args: -cp /media/WD4TB3/svtoolkit/lib/SVToolkit.jar:/media/WD4TB3/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/media/WD4TB3/svtoolkit/lib/gatk/Queue.jar -S /media/WD4TB3/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage1.q -S /media/WD4TB3/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q -S /media/WD4TB3/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q -S /media/WD4TB3/svtoolkit/qscript/SVQScript.q -gatk /media/WD4TB3/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -jobLogDir JAK3project/cnv_stage1/seq_1/logs -memLimit 2.0 -jobRunner Lsf706 -gatkJobRunner Lsf706 -run -sequenceName 1 -runDirectory JAK3project/cnv_stage1/seq_1 -sentinelFile JAK3project/cnv_sentinel_files/stage_1_seq_1.sent --disableJobReport -configFile /media/WD4TB3/svtoolkit/conf/genstrip_parameters.txt -R data/human_g1k_v37.fasta -genomeMaskFile data/human_g1k_v37.svmask.fasta -genderMapFile data/geneder1000GandMysamples.map -md JAK3project/metadata -disableGATKTraversal -I JAK3project/bam_headers/merged_headers.bam -intervalList 1 -scannedWindowsVcfFile JAK3project/cnv_stage1/seq_1/seq_1.sites.vcf -tilingWindowSize 5000 -tilingWindowOverlap 2500 -maximumReferenceGapLength 2500 INFO 20:42:15,478 HelpFormatter - Executing as [email protected] on Linux 3.8.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_65-b17. INFO 20:42:15,478 HelpFormatter - Date/Time: 2015/03/28 20:42:15 INFO 20:42:15,478 HelpFormatter - ---------------------------------------------------------------------- INFO 20:42:15,478 HelpFormatter - ---------------------------------------------------------------------- INFO 20:42:15,485 QCommandLine - Scripting CNVDiscoveryStage1 INFO 20:42:15,632 QCommandLine - Added 2 functions INFO 20:42:15,632 QGraph - Generating graph. INFO 20:42:15,642 QGraph - Running jobs. ERROR 20:42:15,729 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.<clinit>(LibBat.java:91) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(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.newRunner(QGraph.scala:684) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) INFO 20:42:15,730 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

I read here http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_QCommandLine.html that I need to set
-jobRunner workflow_manager \ -gatkJobRunner workflow_manager \
But I don't know how my "workflow_manager" file should look like! Are these arguments going to solve my problem and if so how should I do it?

Thanks,
Reza

Answers

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    It's there on the same page a bit further down:

    Supported workflow managers
    Queue has built-in support for LSF 7. For other workflow managers, you should generally try to use the Drmaa interface (Drmaa is a portable interface for workflow managers in the style of LSF and SGE).

    Queue (and the Genome STRiP Queue scripts) have some built-in options that understand how to pass certain arguments to LSF, but it is generally better practice to use the Drmaa job runner and use -jobNative to pass the necessary arguments to your workflow manager.

    LSF 7.0
    To use LSF 7, specify -jobRunner Lsf706.

    LSF 9.x
    To use LSF 9, specify -jobRunner Drmaa from an LSF execution host configured to use LSF 9.

    SGE
    To use SGE, specify -jobRunner Drmaa from an SGE execution host.

  • alirezakjalirezakj Member
    edited March 2015

    I added the option -jobRunner Drmaa but I get and error saying:

    ERROR 10:43:59,125 QGraph - Uncaught error running jobs. java.lang.UnsatisfiedLinkError: Unable to load library 'drmaa': libdrmaa.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 com.sun.jna.Native.register(Native.java:1018) at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.LibDrmaa.<clinit>(LibDrmaa.java:35) at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.init(JnaSession.java:54) at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobManager.init(DrmaaJobManager.scala:44) at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:409) at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:406) at scala.collection.immutable.List.foreach(List.scala:318) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:406) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) INFO 10:43:59,126 QCommandLine - Done with errors Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load library 'drmaa': libdrmaa.so: cannot open shared object file: No such file or directory

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    Which workflow manager are you trying to use? Does it support drmaa ?
    The code is looking for libdrmaa.so on your LD_LIBRARY_PATH and not finding it.

    If LSF9, you may need to install LSF drmaa support separately.

  • alirezakjalirezakj Member
    edited March 2015

    My workflow manger is SGE, I installed it this way:
    sudo apt-get install gridengine-master gridengine-exec gridengine-common gridengine-qmon gridengine-client gridengine-drmaa-dev libdrmaa-java

    But I had this error E: Unable to locate package gridengine-drmaa-dev

    Post edited by alirezakj on
  • alirezakjalirezakj Member

    I Installed pbs-drmaa-dev and the error is changed to:

    ERROR 15:25:21,201 Retry - Caught error during attempt 1 of 4. org.broadinstitute.gatk.queue.QException: Unable to submit job: No active DRMAA session. at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:89) at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85) at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85) at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49) at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85) at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    Depending on your workflow manager and local configuration, you probably need to specify additional parameters, which you would generally do with (perhaps multiple) -jobNative "value" arguments.
    These are passed directly to the workflow manager. So if you know how to submit the job from the command line, you will generally need to supply most of the same arguments using -jobNative.

  • alirezakjalirezakj Member

    Sorry Bob, I'm not very familiar with grid computing! My workflow manager is SGE and my configurations for SGE is pretty much as default with my host name as my IP address! I don't know how to see the full option list for -jobNative and what to set it as, I am running these on an Ubuntu server with 12CPU cores and 64Gb RAM!

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    I use LSF more than SGE, so maybe somebody else can contribute suggestions.

    If you run Queue without "-run", then it will do a dry run and just print the commands it would execute (but not actually run them).
    I would do this, and then see if you can qsub the command directly and figure out what settings are needed to get qsub to run from the command line. I believe this can vary based on how SGE is configured. Then you just need to translate that command line into -jobNative arguments.

  • jfarrelljfarrell Member ✭✭

    I have the CNV Discovery working with SGE on our cluster.

    Besides adding -jobRunner Drmaa to the commandline, the LD_LIBRARY_PATH also needs to be updated to point to the libdrmaa libraries.

    On our cluster....

    LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/ogs-ge2011.11.p1/sge_root/lib/linux-x64/

     ls -lt /usr/local/ogs-ge2011.11.p1/sge_root/lib/linux-x64/
    
            lrwxrwxrwx 1 root root      15 Mar 23  2013 libdrmaa.so -> libdrmaa.so.1.0
            -rwxr-xr-x 1 root root 2033525 Mar 23  2013 libdrmaa.so.1.0
            -rwxr-xr-x 1 root root   70991 Mar 23  2013 libXltree.so
    
  • jfarrelljfarrell Member ✭✭

    Actually, I spoke too soon.

    The jobs submitted OK but I got these error messages:

        INFO  14:16:51,419 HelpFormatter - Date/Time: 2015/04/08 14:16:51
        INFO  14:16:51,419 HelpFormatter - ----------------------------------------------------------------------
        INFO  14:16:51,419 HelpFormatter - ----------------------------------------------------------------------
        INFO  14:16:51,426 QCommandLine - Scripting CNVDiscoveryStage1
        INFO  14:16:51,929 QCommandLine - Added 2 functions
        INFO  14:16:51,929 QGraph - Generating graph.
        INFO  14:16:51,961 QGraph - Running jobs.
        ERROR 14:16:52,129 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.<clinit>(LibBat.java:91)
                at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237)
                at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala)
                at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(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.newRunner(QGraph.scala:684)
                at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433)
                at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
                at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
                at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
                at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
                at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
                at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
        INFO  14:16:52,130 QCommandLine - Done with errors
        Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory
                at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
                at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
                at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
                at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91)
                at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237)
                at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala)
                at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48)
                at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36)
                at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34)
                at org.broadinstitute.gatk.queue.engine.QGraph.newRunner(QGraph.scala:684)
                at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433)
                at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
                at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
                at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
                at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
                at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
                at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
        INFO  14:16:52,151 QCommandLine - Shutting down jobs. Please wait...
        INFO  14:16:58,173 QGraph - Writing incremental jobs reports...
        INFO  14:16:58,181 QGraph - 758 Pend, 81 Run, 3 Fail, 2 Done
    
  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    You need to specify -gatkJobRunner in addition to -jobRunner.

  • jfarrelljfarrell Member ✭✭

    The other GenomeSTRiP tasks run fine on SGE (PreProcessing, SVDIscovery and SV_Genotyper).

    It it just the CNVDiscoveryPipeline that is having the problem.

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    Yes. This is because the CNV pipeline runs Queue jobs recursively. The whole reason there are two arguments (-jobRunner and -gatkJobRunner) is because within the Queue scripts we cannot access the -jobRunner argument, which is available only to the Queue engine. So when the CNV pipeline launches a recursive job, it uses -gatkJobRunner (which will default to LSF706 if you do not override it).

  • jfarrelljfarrell Member ✭✭

    Thanks Bob! The CNV script run is now running fine on SGE when both those arguments are specified along with the updated LD_LIBRARY_PATH.

  • jfarrelljfarrell Member ✭✭

    There is another error that is generated later on during the run....

    ERROR 23:31:47,518 QGraph - Uncaught error running jobs.
    org.ggf.drmaa.DrmCommunicationException: cannot register event client. Only 99 event clients are allowed in the system

    According to this article (https://github.com/PacificBiosciences/SMRT-Analysis/wiki/When-using-the-sync-option-in-SGE,-you-may-see-errors), the SGE parameter MAX_DYN_EC on SGE would need to be increased to a larger number ( qconf -mconf qmaster_params MAX_DYN_EC=1000).

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    That's a new one on me. Perhaps you have more then 99 Queue processes running in parallel? Just a guess.

  • Weijian_leafWeijian_leaf China,DenmarkMember
    edited April 2015

    @bhandsaker said:
    That's a new one on me. Perhaps you have more then 99 Queue processes running in parallel? Just a guess.

    Hi bhandsaker and all,
    When I ran the GenomeStrip on our cluster, I also got the same kind of error and I installed the Drmaa, changed my bashrc and used option "-jobRunner Drmaa", "-gatkJobRunner Drmaa".
    Unfortunately, in my situation, the CNVpip still could not work. The error is like below, hopefully this error log can help. Because I am not very familiar with the computing cluster, could someone help? Thanks lot.

    java: error: Parsing error at unrecognized key: ExclusiveUser
    java: error: Parse error in file /opt/slurm/etc/slurm.conf line 154: " ExclusiveUser=yes AllowAccounts=ripsych"
    java: error: Parsing error at unrecognized key: ExclusiveUser
    java: error: Parse error in file /opt/slurm/etc/slurm.conf line 155: " ExclusiveUser=yes AllowAccounts=ripsych"
    java: error: Parsing error at unrecognized key: ExclusiveUser
    java: error: Parse error in file /opt/slurm/etc/slurm.conf line 156: " ExclusiveUser=yes AllowAccounts=ripsych"
    java: error: Parsing error at unrecognized key: ExclusiveUser
    java: error: Parse error in file /opt/slurm/etc/slurm.conf line 157: " ExclusiveUser=yes AllowAccounts=ripsych"
    java: error: Unable to establish controller machine
    ERROR 12:07:10,065 Retry - Caught error during attempt 1 of 4.
    org.ggf.drmaa.InternalException: slurm_submit_batch_job: No error
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.checkError(JnaSession.java:400)
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.checkError(JnaSession.java:392)
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.runJob(JnaSession.java:79)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:87)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
    at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434)
    at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
    at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
    ERROR 12:07:10,068 Retry - Retrying in 1.0 minute.
    java: error: Unable to establish controller machine
    ERROR 12:08:10,072 Retry - Caught error during attempt 2 of 4.
    org.ggf.drmaa.InternalException: slurm_submit_batch_job: No such file or directory
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.checkError(JnaSession.java:400)
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.checkError(JnaSession.java:392)
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.runJob(JnaSession.java:79)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:87)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85)
    at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
    at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434)
    at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
    at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
    ERROR 12:08:10,075 Retry - Retrying in 5.0 minutes.

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    It looks like it is complaining about a syntax error in slurm.conf.

  • traceyctraceyc Member

    Hi,

    After specifying -jobRunner Drmaa and -gatkJobRunner Drmaa and changing LD_LIBRARY_PATH for my CNV Discovery script, when I try to run the script, I get the error
    "ERROR 22:38:50,102 QGraph - Uncaught error running jobs.
    java.lang.UnsatisfiedLinkError: Unable to load library 'drmaa': libdrmaa.so: cannot open shared object file: No such file or directory"
    as seen below. The cluster I use has the workflow manager SGE and when I check the updated LD_LIBRARY_PATH, I can see the needed libdrmaa.so file so I'm not sure why libdrmaa.so cannot be found. Do you have any suggestions for what I can try doing?

    I also get the error
    "ERROR 10:01:30,410 FunctionEdge - Error: samtools index test_30bams_sl/bam_headers/merged_headers.bam
    ERROR 10:01:30,422 FunctionEdge - Contents of /u/project/zarlab/traceyc/svtoolkit/first/test_30bams_sl/logs/CNVDiscoveryPipeline-2.out:
    /u/scratch/t/traceyc/.exec6239455173303316061: line 2: samtools: command not found"
    even though I have samtools-1.2 in my PATH and have used samtools before without problems.

    Please let me know what I can do to avoid these errors. Thank you!
    Tracey

    INFO 22:36:46,896 QScriptManager - Compiling 4 QScripts
    INFO 22:37:09,830 QScriptManager - Compilation complete
    INFO 22:37:10,041 HelpFormatter - ----------------------------------------------------------------------
    INFO 22:37:10,042 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/05/15 09:12:56
    INFO 22:37:10,042 HelpFormatter - Copyright (c) 2012 The Broad Institute
    INFO 22:37:10,042 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 22:37:10,043 HelpFormatter - Program Args: -cp /u/home/t/traceyc/project-zarlab/svtoolkit/lib/SVToolkit.jar:/u/home/t/traceyc/project-zarlab/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/u/home/t/traceyc/project-zarlab/svtoolkit/lib/gatk/Queue.jar -S /u/home/t/traceyc/project-zarlab/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage1.q -S /u/home/t/traceyc/project-zarlab/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q -S /u/home/t/traceyc/project-zarlab/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q -S /u/home/t/traceyc/project-zarlab/svtoolkit/qscript/SVQScript.q -gatk /u/home/t/traceyc/project-zarlab/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -jobLogDir test_30bams/cnv_stage1/seq_GL000233.1/logs -memLimit 2.0 -jobRunner Drmaa -gatkJobRunner Drmaa -run -sequenceName GL000233.1 -runDirectory test_30bams/cnv_stage1/seq_GL000233.1 -sentinelFile test_30bams/cnv_sentinel_files/stage_1_seq_GL000233.1.sent --disableJobReport -configFile conf/genstrip_mod1_parameters.txt -R /u/home/t/traceyc/project-zarlab/svtoolkit/reference_metadata_bundles/1000G_phase3/converted_human_g1k_hs37d5.fasta -ploidyMapFile /u/home/t/traceyc/project-zarlab/svtoolkit/reference_metadata_bundles/1000G_phase3/human_g1k_hs37d5.ploidymap.txt -genderMapFile /u/home/t/traceyc/project-zarlab/svtoolkit/first/first_data/1kgp30.gendermap.txt -md test_30bams/metadata -disableGATKTraversal -I test_30bams/bam_headers/merged_headers.bam -intervalList GL000233.1 -scannedWindowsVcfFile test_30bams/cnv_stage1/seq_GL000233.1/seq_GL000233.1.sites.vcf.gz -tilingWindowSize 5000 -tilingWindowOverlap 2500 -maximumReferenceGapLength 2500
    INFO 22:37:10,046 HelpFormatter - Executing as [email protected] on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_05_14_07_23-b00.
    INFO 22:37:10,046 HelpFormatter - Date/Time: 2015/10/25 22:37:10
    INFO 22:37:10,047 HelpFormatter - ----------------------------------------------------------------------
    INFO 22:37:10,047 HelpFormatter - ----------------------------------------------------------------------
    INFO 22:37:10,060 QCommandLine - Scripting CNVDiscoveryStage1
    INFO 22:37:10,342 QCommandLine - Added 2 functions
    INFO 22:37:10,343 QGraph - Generating graph.
    INFO 22:37:10,362 QGraph - Running jobs.
    ERROR 22:37:10,502 QGraph - Uncaught error running jobs.
    java.lang.UnsatisfiedLinkError: Unable to load library 'drmaa': libdrmaa.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 com.sun.jna.Native.register(Native.java:1018)
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.LibDrmaa.(LibDrmaa.java:35)
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.init(JnaSession.java:54)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobManager.init(DrmaaJobManager.scala:44)
    at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:409)
    at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:406)
    at scala.collection.immutable.List.foreach(List.scala:318)
    at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:406)
    at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
    at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
    INFO 22:37:10,505 QCommandLine - Done with errors
    Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load library 'drmaa': libdrmaa.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 com.sun.jna.Native.register(Native.java:1018)
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.LibDrmaa.(LibDrmaa.java:35)
    at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.init(JnaSession.java:54)
    at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobManager.init(DrmaaJobManager.scala:44)
    at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:409)
    at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:406)
    at scala.collection.immutable.List.foreach(List.scala:318)
    at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:406)
    at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
    at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
    INFO 22:37:10,518 QCommandLine - Shutting down jobs. Please wait...

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    It would be nice if you could post this as a new question, since this discussion is kind of a grab bag of random problems.

    I suspect your problem is that you are not passing the needed -jobNative arguments in your environment.
    Most SGE installations require -jobNative "-V -cwd". You can also try -jobRunner GridEngine, which sets -V.
    If your are losing your LD_LIBRARY_PATH (because some SGE installations do not allow LD_LIBRARY_PATH to be inherited, period), then one workaround is to use a (new in r1611) argument:

    -jobWrapperScript path_to_wrapper_script

    This is a way to inject a wrapper script around all jobs that are submitted to the workflow manager (e.g. SGE).
    You can set environment variables, LD_LIBRARY_PATH, etc., inside this wrapper script, then execute the command using, e.g.:

    #/bin/bash export LD_LIBRARY_PATH=... ${@}

  • traceyctraceyc Member

    Thanks so much for the help! It seems to work now when I add -jobNative. I will repost my original comment as a new question.

  • kkyung412kkyung412 koreaMember

    Hi Bob,

    While running CNV discovery with the command below:

    classpath="/shared/tools/svtoolkit/lib/SVToolkit.jar:/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/shared/tools/svtoolkit/lib/gatk/Queue.jar" java -Xmx4g -cp ${classpath} \ org.broadinstitute.gatk.queue.QCommandLine \ -S /shared/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q \ -S /shared/tools/svtoolkit/qscript/SVQScript.q \ -cp ${classpath} \ -gatk /shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar \ -configFile /shared/tools/svtoolkit/conf/genstrip_parameters.txt \ -R /shared/data/GATKbundle/hg19.fasta \ -I /shared/home/kkyung412/KPGP_TransposableElement_2015_IRCGP/WGS/THERAGEN/KPGP-00009.recalibrated.bam \ -md input_metadata_directory \ -genderMapFile /shared/tools/svtoolkit/gender_map_file.txt \ -ploidyMapFile /shared/tools/svtoolkit/humgen_g1k_v37_ploidy.map\ -runDirectory run1 \ -jobLogDir run1/logs \ -jobRunner Drmaa \ -gatkJobRunner Drmaa \ -tilingWindowSize 1000 \ -tilingWindowOverlap 500 \ -maximumReferenceGapLength 1000 \ -boundaryPrecision 100 \ -minimumRefinedLength 500 \ -run
    I ran into an error saying:
    Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/shared/tmp INFO 15:09:52,163 QScriptManager - Compiling 2 QScripts INFO 15:10:26,297 QScriptManager - Compilation complete INFO 15:10:26,597 HelpFormatter - ---------------------------------------------------------------------- INFO 15:10:26,597 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/10/04 09:18:40 INFO 15:10:26,598 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 15:10:26,598 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 15:10:26,600 HelpFormatter - Program Args: -S /shared/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q -S /shared/tools/svtoolkit/qscript/SVQScript.q -cp /shared/tools/svtoolkit/lib/SVToolkit.jar:/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/shared/tools/svtoolkit/lib/gatk/Queue.jar -gatk /shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /shared/tools/svtoolkit/conf/genstrip_parameters.txt -R /shared/data/GATKbundle/hg19.fasta -I /shared/home/kkyung412/KPGP_TransposableElement_2015_IRCGP/WGS/THERAGEN/KPGP-00009.recalibrated.bam -md input_metadata_directory -genderMapFile /shared/tools/svtoolkit/gender_map_file.txt -ploidyMapFile /shared/tools/svtoolkit/humgen_g1k_v37_ploidy.map -runDirectory run1 -jobLogDir run1/logs -jobRunner Drmaa -gatkJobRunner Drmaa -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500 -run INFO 15:10:26,601 HelpFormatter - Executing as kkyung41[email protected] on Linux 3.13.0-43-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32. INFO 15:10:26,601 HelpFormatter - Date/Time: 2015/10/28 15:10:26 INFO 15:10:26,602 HelpFormatter - ---------------------------------------------------------------------- INFO 15:10:26,603 HelpFormatter - ---------------------------------------------------------------------- INFO 15:10:26,618 QCommandLine - Scripting CNVDiscoveryPipeline INFO 15:10:28,335 QCommandLine - Added 255 functions INFO 15:10:28,336 QGraph - Generating graph. INFO 15:10:28,605 QGraph - Running jobs. ERROR 15:10:28,694 QGraph - Uncaught error running jobs. java.lang.UnsatisfiedLinkError: Unable to load library 'drmaa': libdrmaa.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 com.sun.jna.Native.register(Native.java:1018) at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.LibDrmaa.<clinit>(LibDrmaa.java:35) at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.init(JnaSession.java:54) at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobManager.init(DrmaaJobManager.scala:44) at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:409) at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:406) at scala.collection.immutable.List.foreach(List.scala:318) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:406) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) INFO 15:10:28,696 QCommandLine - Done with errors INFO 15:10:28,755 QGraph - ------- INFO 15:10:28,769 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/shared/tmp' '-cp' '/shared/tools/svtoolkit/lib/SVToolkit.jar:/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/shared/tools/svtoolkit/lib/gatk/Queue.jar' '-cp' '/shared/tools/svtoolkit/lib/SVToolkit.jar:/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/shared/tools/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.gatk.queue.QCommandLine' '-cp' '/shared/tools/svtoolkit/lib/SVToolkit.jar:/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/shared/tools/svtoolkit/lib/gatk/Queue.jar' '-S' 'qscript/discovery/cnv/CNVDiscoveryStage1.q' '-S' 'qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' 'qscript/discovery/cnv/CNVDiscoveryGenotyper.q' '-S' 'qscript/SVQScript.q' '-gatk' '/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar' '-jobLogDir' 'run1/cnv_stage1/seq_chr11/logs' '-memLimit' '2.0' '-jobRunner' 'Drmaa' '-gatkJobRunner' 'Drmaa' -run '-sequenceName' 'chr11' '-runDirectory' 'run1/cnv_stage1/seq_chr11' '-sentinelFile' 'run1/cnv_sentinel_files/stage_1_seq_chr11.sent' --disableJobReport '-configFile' '/shared/tools/svtoolkit/conf/genstrip_parameters.txt' '-R' '/shared/data/GATKbundle/hg19.fasta' '-ploidyMapFile' '/shared/tools/svtoolkit/humgen_g1k_v37_ploidy.map' '-genderMapFile' '/shared/tools/svtoolkit/gender_map_file.txt' '-md' 'input_metadata_directory' -disableGATKTraversal '-I' 'run1/bam_headers/merged_headers.bam' '-intervalList' 'chr11' '-scannedWindowsVcfFile' 'run1/cnv_stage1/seq_chr11/seq_chr11.sites.vcf.gz' '-tilingWindowSize' '1000' '-tilingWindowOverlap' '500' '-maximumReferenceGapLength' '1000' INFO 15:10:28,771 QGraph - Log: /shared/tools/svtoolkit/run1/logs/CNVDiscoveryPipeline-4.out INFO 15:10:28,771 QGraph - ------- INFO 15:10:28,780 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/shared/tmp' '-cp' '/shared/tools/svtoolkit/lib/SVToolkit.jar:/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/shared/tools/svtoolkit/lib/gatk/Queue.jar' '-cp' '/shared/tools/svtoolkit/lib/SVToolkit.jar:/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/shared/tools/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.gatk.queue.QCommandLine' '-cp' '/shared/tools/svtoolkit/lib/SVToolkit.jar:/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/shared/tools/svtoolkit/lib/gatk/Queue.jar' '-S' 'qscript/discovery/cnv/CNVDiscoveryStage1.q' '-S' 'qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' 'qscript/discovery/cnv/CNVDiscoveryGenotyper.q' '-S' 'qscript/SVQScript.q' '-gatk' '/shared/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar' '-jobLogDir' 'run1/cnv_stage1/seq_chr5/logs' '-memLimit' '2.0' '-jobRunner' 'Drmaa' '-gatkJobRunner' 'Drmaa' -run '-sequenceName' 'chr5' '-runDirectory' 'run1/cnv_stage1/seq_chr5' '-sentinelFile' 'run1/cnv_sentinel_files/stage_1_seq_chr5.sent' --disableJobReport '-configFile' '/shared/tools/svtoolkit/conf/genstrip_parameters.txt' '-R' '/shared/data/GATKbundle/hg19.fasta' '-ploidyMapFile' '/shared/tools/svtoolkit/humgen_g1k_v37_ploidy.map' '-genderMapFile' '/shared/tools/svtoolkit/gender_map_file.txt' '-md' 'input_metadata_directory' -disableGATKTraversal '-I' 'run1/bam_headers/merged_headers.bam' '-intervalList' 'chr5' '-scannedWindowsVcfFile' 'run1/cnv_stage1/seq_chr5/seq_chr5.sites.vcf.gz' '-tilingWindowSize' '1000' '-tilingWindowOverlap' '500' '-maximumReferenceGapLength' '1000' INFO 15:10:28,780 QGraph - Log: /shared/tools/svtoolkit/run1/logs/CNVDiscoveryPipeline-8.out Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load library 'drmaa': libdrmaa.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 com.sun.jna.Native.register(Native.java:1018) at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.LibDrmaa.<clinit>(LibDrmaa.java:35) at org.broadinstitute.gatk.utils.jna.drmaa.v1_0.JnaSession.init(JnaSession.java:54) at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobManager.init(DrmaaJobManager.scala:44) at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:409) at org.broadinstitute.gatk.queue.engine.QGraph$$anonfun$runJobs$1.apply(QGraph.scala:406) at scala.collection.immutable.List.foreach(List.scala:318) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:406) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) INFO 15:10:28,788 QCommandLine - Shutting down jobs. Please wait...

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    Please delete this and post as a new question.

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