Re: [svtoolkit-help] How to run genomostrip2 on personal desktop?

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The short answer is that if you just remove -jobRunner and 
-gatkJobRunner, then Queue will run all of the processing jobs 
synchronously as child processes.

However, the longer answer is that you won't be able to do more than toy 
scenarios in this way.
To get good results, you need to process a number of genomes together.
It is possible to run with 30-50 genomes, but our experience has been 
that the results in this case are OK, but not great (false discovery 
rate around 5-10%).
With 100-200 genomes, results are much improved (< 5% FDR) and with 
500-1000 genomes the results get noticeably better (we can often get 
2-3% FDR).
Processing even 30-50 genomes on a personal desktop seems pretty 
daunting, since it looks like you are processing human data.

-Bob

On 4/4/15 6:38 PM, 周在威 wrote:
> 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
>
>
>
>
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