Re: [svtoolkit-help] discovery.sh produce only one file
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Re: [svtoolkit-help] discovery.sh produce only one file
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From: Boel B. <bry...@gm...> - 2012-01-31 14:24:08
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This question has already been answered using my other registered email. Thanks. Den 30 januari 2012 12:05 skrev Boel Brynedal <bry...@br...>: > Hi, > > Very glad to find out that your program is out and ready to be used, exactly what I was looking for. > > When running the discovery.sh test I get the message that: "Error: test results do not match benchmark data". > I quick look revealed that only one result file was produced (test1.discovery.vcf) while the other one (test1.genotypes.vcf) is missing. Did something go wrong, or should only one file be produced? > > Output fr discovery.sh: > $ ./discovery.sh > SVToolkit version 1.03 (build 619) > Build date: 2011/02/12 17:23:22 > Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP > INFO 11:37:59,050 QScriptManager - Compiling 2 QScripts > INFO 11:38:05,021 QScriptManager - Compilation complete > INFO 11:38:10,911 HelpFormatter - --------------------------------------------------------- > INFO 11:38:10,911 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine > INFO 11:38:10,912 HelpFormatter - Program Args: -S /scratch/bb447/svtoolkit/qscript/SVPreprocess.q -S /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -I data/installtest.bam -run > INFO 11:38:10,912 HelpFormatter - Date/Time: 2012/01/30 11:38:10 > INFO 11:38:10,912 HelpFormatter - --------------------------------------------------------- > INFO 11:38:10,912 HelpFormatter - --------------------------------------------------------- > INFO 11:38:10,913 QCommandLine - Scripting SVPreprocess > INFO 11:38:11,049 QCommandLine - Added 7 functions > INFO 11:38:11,049 QGraph - Generating graph. > INFO 11:38:11,073 QGraph - Running jobs. > INFO 11:38:11,080 QGraph - Deleting intermediate files. > INFO 11:38:11,081 QCommandLine - Done > INFO 11:38:13,403 QScriptManager - Compiling 2 QScripts > INFO 11:38:18,509 QScriptManager - Compilation complete > INFO 11:38:21,037 HelpFormatter - --------------------------------------------------------- > INFO 11:38:21,037 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine > INFO 11:38:21,037 HelpFormatter - Program Args: -S /scratch/bb447/svtoolkit/qscript/SVDiscovery.q -S /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I data/installtest.bam -O test1.discovery.vcf -run > INFO 11:38:21,038 HelpFormatter - Date/Time: 2012/01/30 11:38:21 > INFO 11:38:21,038 HelpFormatter - --------------------------------------------------------- > INFO 11:38:21,038 HelpFormatter - --------------------------------------------------------- > INFO 11:38:21,039 QCommandLine - Scripting SVDiscovery > INFO 11:38:21,183 QCommandLine - Added 2 functions > INFO 11:38:21,184 QGraph - Generating graph. > INFO 11:38:21,196 QGraph - Running jobs. > INFO 11:38:21,250 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -md test1/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 11:38:21,250 ShellJobRunner - Output written to /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-1.out > INFO 11:38:48,558 ShellJobRunner - Done: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -md test1/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 11:38:48,562 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" > INFO 11:38:48,562 ShellJobRunner - Output written to /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-2.out > INFO 11:38:54,842 ShellJobRunner - Done: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" > INFO 11:38:54,843 QGraph - Deleting intermediate files. > INFO 11:38:54,844 QCommandLine - Done > Files - and benchmark/test1.discovery.vcf differ > Error: test results do not match benchmark data > > Please let me know if there is any more information that might be helpful. > Thanks, > Boel > > --~*~**~***~*~***~**~*~-- > Boel Brynedal, PhD. > Post Doctoral Associate > Department of Neurology & Department of Genetics, > Yale Medical School, New Haven, CT. > Medical and Population Genetics, The Broad Institute, Cambridge, MA. > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
