svtoolkit-help

[svtoolkit-help] GenomeSTRiP v2

[shiyujian2 <shi...@ge...>]

Hello,

I'm running into difficulties trying to run CNVDiscovery pipeline with svtoolkit_2.00.1529 version. I copied my command as below 

classpath=/xxx/svtoolkit/lib/SVToolkit.jar:/xxx/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/xxx/svtoolkit/lib/gatk/Queue.jar
export PATH=/xxx/R-3.0.2/bin/:/xxx/svtoolkit/:/xxx/svtoolkit/bwa/:$PATH; export SV_DIR=/xxx/svtoolkit; 
/xxx/bin/software/jre1.7.0_25/bin/java -Xmx10g -XX:+UseParallelOldGC -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 
-Djava.io.tmpdir=/xxx/.queue/tmp -cp ${classpath} 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 
-R /xxx/hg19.fa 
-I /xxx/discovery.bams.args.list 
-genderMapFile /xxx/gender.map 
-md /xxx/metadata 
-configFile /xxx/conf/genstrip_parameters.txt 
-runDirectory /xxx/cnvdiscovery 
-genomeMaskFile /xxx/svtoolkit/database/hg19_mask101.fasta 
-intervalList chr1:1-4010001 
-tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500 
-jobLogDir /xxx/cnvdiscovery/logs
-run 



Error from Shell CNVDiscoveryPipeline run

INFO  14:48:37,214 HelpFormatter - Date/Time: 2015/03/09 14:48:37
INFO  14:48:37,214 HelpFormatter - ----------------------------------------------------------------------
INFO  14:48:37,214 HelpFormatter - ----------------------------------------------------------------------
INFO  14:48:37,221 QCommandLine - Scripting CNVDiscoveryStage1
INFO  14:48:37,394 QCommandLine - Added 2 functions
INFO  14:48:37,395 QGraph - Generating graph.
INFO  14:48:37,406 QGraph - Running jobs.
ERROR 14:48:37,833 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  14:48:37,834 QCommandLine - Done with errors

I am running on SGE cluster system, can I handle this problem through any parameters?

Thanks,
Yujian

Re: [svtoolkit-help] GenomeSTRiP v2

[Bob H. <han...@br...>]

There is some documentation on how to use SGE here:
http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_QCommandLine.html
Also see the job

You need to supply "-jobRunner Drmaa" and for the CNV pipeline also 
"-gatkJobRunner Drmaa".
Depending on your SGE configuration, you may also need to make liberal 
use of -jobNative to pass additional arguments.
For example
-jobNative "-q myqueue"
-jobNative "-l virtual_free=8000m"
etc.

-Bob

On 3/9/15 4:02 AM, shiyujian2 wrote:
> Hello,
> I'm running into difficulties trying to run CNVDiscovery pipeline with 
> svtoolkit_2.00.1529 
> <http://www.broadinstitute.org/software/genomestrip/download/72/svtoolkit_2.00.1529.tar.gz?redirect=node/2> version. 
> I copied my command as below
> classpath=/xxx/svtoolkit/lib/SVToolkit.jar:/xxx/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/xxx/svtoolkit/lib/gatk/Queue.jar
> export 
> PATH=/xxx/R-3.0.2/bin/:/xxx/svtoolkit/:/xxx/svtoolkit/bwa/:$PATH; 
> export SV_DIR=/xxx/svtoolkit;
> /xxx/bin/software/jre1.7.0_25/bin/java -Xmx10g -XX:+UseParallelOldGC 
> -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10
> -Djava.io.tmpdir=/xxx/.queue/tmp -cp ${classpath} 
> org.broadinstitute.gatk.queue.QCommandLine
> -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q
> -S ${SV_DIR}/qscript/SVQScript.q
> -cp ${classpath}
> -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar
> -R /xxx/hg19.fa
> -I /xxx/discovery.bams.args.list
> -genderMapFile /xxx/gender.map
> -md /xxx/metadata
> -configFile /xxx/conf/genstrip_parameters.txt
> -runDirectory /xxx/cnvdiscovery
> -genomeMaskFile /xxx/svtoolkit/database/hg19_mask101.fasta
> -intervalList chr1:1-4010001
> -tilingWindowSize 1000 -tilingWindowOverlap 500 
> -maximumReferenceGapLength 1000 -boundaryPrecision 100 
> -minimumRefinedLength 500
> -jobLogDir /xxx/cnvdiscovery/logs
> -run
> Error from Shell CNVDiscoveryPipeline run
> INFO 14:48:37,214 HelpFormatter - Date/Time: 2015/03/09 14:48:37
> INFO  14:48:37,214 HelpFormatter - 
> ----------------------------------------------------------------------
> INFO  14:48:37,214 HelpFormatter - 
> ----------------------------------------------------------------------
> INFO  14:48:37,221 QCommandLine - Scripting CNVDiscoveryStage1
> INFO  14:48:37,394 QCommandLine - Added 2 functions
> INFO  14:48:37,395 QGraph - Generating graph.
> INFO  14:48:37,406 QGraph - Running jobs.
> ERROR 14:48:37,833 QGraph - Uncaught error running jobs.
> java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': 
> liblsf.so: cannot open shared object file: No such file or directory
>         at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
>         at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
>         at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
>         at 
> org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91)
>         at 
> org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<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  14:48:37,834 QCommandLine - Done with errors
> I am running on SGE cluster system, can I handle this problem through 
> any parameters?
> Thanks,
> Yujian
>
>
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