[svtoolkit-help] How to run genomostrip2 on personal desktop?
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[svtoolkit-help] How to run genomostrip2 on personal desktop?
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From: 周在威 <zho...@16...> - 2015-04-04 22:38:28
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Hi all, I ran in to errors when run genomestrip2 on my personal desktop not cloud system, the error as follows: INFO 18:32:25,780 QScriptManager - Compiling 4 QScripts INFO 18:32:31,567 QScriptManager - Compilation complete INFO 18:32:31,611 HelpFormatter - ---------------------------------------------------------------------- INFO 18:32:31,611 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/02/06 10:59:46 INFO 18:32:31,611 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 18:32:31,611 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 18:32:31,611 HelpFormatter - Program Args: -cp /media/D/genomestrip/svtoolkit/lib/SVToolkit.jar:/media/D/genomestrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/media/D/genomestrip/svtoolkit/lib/gatk/Queue.jar -S /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage1.q -S /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q -S /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q -S /media/D/genomestrip/svtoolkit/qscript/SVQScript.q -gatk /media/D/genomestrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -jobLogDir run1/cnv_stage1/seq_GL000221.1/logs -memLimit 2.0 -jobRunner Lsf706 -gatkJobRunner Lsf706 -run -sequenceName GL000221.1 -runDirectory run1/cnv_stage1/seq_GL000221.1 -sentinelFile run1/cnv_sentinel_files/stage_1_seq_GL000221.1.sent --disableJobReport -configFile /media/D/genomestrip/cmt/conf/genstrip_parameters.txt -R /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta -ploidyMapFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt -genomeMaskFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta -genomeMaskFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.lcmask.fasta -copyNumberMaskFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gcmask.fasta -readDepthMaskFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.rdmask.bed -genderMaskBedFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gendermask.bed -vdjBedFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.vdjregions.bed -genderMapFile /media/D/genomestrip/Homo_sapiens_assembly19/cmt_gender.map -md cmt/metadata -disableGATKTraversal -I run1/bam_headers/merged_headers.bam -intervalList GL000221.1 -scannedWindowsVcfFile run1/cnv_stage1/seq_GL000221.1/seq_GL000221.1.sites.vcf -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 INFO 18:32:31,611 HelpFormatter - Executing as wei@localhost.localdomain on Linux 2.6.32-504.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_65-mockbuild_2014_07_16_06_06-b00. INFO 18:32:31,612 HelpFormatter - Date/Time: 2015/03/27 18:32:31 INFO 18:32:31,612 HelpFormatter - ---------------------------------------------------------------------- INFO 18:32:31,612 HelpFormatter - ---------------------------------------------------------------------- INFO 18:32:31,615 QCommandLine - Scripting CNVDiscoveryStage1 INFO 18:32:31,688 QCommandLine - Added 2 functions INFO 18:32:31,688 QGraph - Generating graph. INFO 18:32:31,694 QGraph - Running jobs. ERROR 18:32:31,726 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$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) INFO 18:32:31,727 QCommandLine - Done with errors Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<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 18:32:31,729 QCommandLine - Shutting down jobs. Please wait... can i disable LSF in any parameters or just impossible to run genomestrip2 on personal desktop? Thanks. Zaiwei |
