Unable to load library 'drmaa': libdrmaa.so error

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$1.apply(QGraph.scala:409)atorg.broadinstitute.gatk.queue.engine.QGraph
anonfun$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$1.apply(QGraph.scala:409)atorg.broadinstitute.gatk.queue.engine.QGraph
anonfun$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...

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