[svtoolkit-help] discovery.sh produce only one file
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[svtoolkit-help] discovery.sh produce only one file
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From: Boel B. <bry...@br...> - 2012-01-30 17:00:31
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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. |
