Re: [svtoolkit-help] discovery.sh only produce one file
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Re: [svtoolkit-help] discovery.sh only produce one file
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From: Bob H. <han...@br...> - 2012-01-30 19:33:33
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Hi, Boel, This is a problem that I think was reported once before (or I ran into it). Ideally, I should be rounding off these values and then the comparisons should pass. You can safely comment out the line in the script that does the diff and carry on. -Bob On 1/30/12 1:43 PM, Boel Brynedal wrote: > Hi, > > Updated to the latest interim version, but get the same error message. > Turns out the only difference is the GSCOHERENCE value > (-3.162711280554605 vs -3.1627112805546047) and the GSCOHFN value > (-0.5271185467591009 vs -0.5271185467591007), see the two rows below. > Might this be an issue? > The file "test1.genotypes.vcf" is not created at all, if it was suppose to. > > Thanks! > Boel > > 1 61722559 DEL_1 T <DEL> . DEPTH;DEPTHPVAL CIEND=-8,8;CIPOS=-8,8;END=61722981;GSCOHERENCE=-3.162711280554605;GSCOHFN=-0.5271185467591009;GSCOHPVALUE=0.901;GSCOORDS=61722491,61722556,61723000,61723144;GSDEPTHCALLTHRESHOLD=0.9600579875024452;GSDEPTHNOBSSAMPLES=5;GSDEPTHNTOTALSAMPLES=5;GSDEPTHOBSSAMPLES=NA07051,NA11830,NA11920,NA12003,NA12249;GSDEPTHPVALUE=0.035631;GSDEPTHPVALUECOUNTS=74,35512,511,321039;GSDEPTHRANKSUMPVALUE=0.9802336;GSDEPTHRATIO=1.3091622731975827;GSDMAX=543;GSDMIN=1;GSDOPT=420;GSDSPAN=443;GSMEMBNPAIRS=6;GSMEMBNSAMPLES=5;GSMEMBOBSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830;GSMEMBPVALUE=0.4945;GSMEMBSTATISTIC=40.43627779276575;GSNDEPTHCALLS=39;GSNPAIRS=6;GSNSAMPLES=5;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=ERR000550,ERR000567,SRR003115,SRR003135,SRR006095,SRR006165;GSREADNAMES=EAS139_44:6:82:100:15931,EAS139_47:7:5:530:8011,SRR003115.6626735,SRR003135.5278653,SRR006095.2235470,SRR006165.7774794;GSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830,NA07051;IMPRECISE;SVLEN=-420;SVTYPE=DEL > > 1 61722559 DEL_1 T <DEL> . DEPTH;DEPTHPVAL CIEND=-8,8;CIPOS=-8,8;END=61722981;GSCOHERENCE=-3.1627112805546047;GSCOHFN=-0.5271185467591007;GSCOHPVALUE=0.901;GSCOORDS=61722491,61722556,61723000,61723144;GSDEPTHCALLTHRESHOLD=0.9600579875024452;GSDEPTHNOBSSAMPLES=5;GSDEPTHNTOTALSAMPLES=5;GSDEPTHOBSSAMPLES=NA07051,NA11830,NA11920,NA12003,NA12249;GSDEPTHPVALUE=0.035631;GSDEPTHPVALUECOUNTS=74,35512,511,321039;GSDEPTHRANKSUMPVALUE=0.9802336;GSDEPTHRATIO=1.3091622731975827;GSDMAX=543;GSDMIN=1;GSDOPT=420;GSDSPAN=443;GSMEMBNPAIRS=6;GSMEMBNSAMPLES=5;GSMEMBOBSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830;GSMEMBPVALUE=0.4945;GSMEMBSTATISTIC=40.43627779276575;GSNDEPTHCALLS=39;GSNPAIRS=6;GSNSAMPLES=5;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=ERR000550,ERR000567,SRR003115,SRR003135,SRR006095,SRR006165;GSREADNAMES=EAS139_44:6:82:100:15931,EAS139_47:7:5:530:8011,SRR003115.6626735,SRR003135.5278653,SRR006095.2235470,SRR006165.7774794;GSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830,NA07051;IMPRECISE;SVLEN=-420;SVTYPE=DEL > > > Den 30 januari 2012 12:18 skrev Bob Handsaker<han...@br...>: >> Hi, Boel, >> I would encourage you to try using the latest interim release. >> These are updates that are missing documentation for some new features >> and occasional incompatibilities, but people have generally been able to >> use them successfully. >> The interim releases are available at >> ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/. >> What would be helpful to diagnose the problem is a manual diff of >> test1.discovery.vcf and benchmark/test1.discovery.vcf. >> There are a couple of lines (like ##fileDate) that are not expected to >> match, but other mismatches are likely indicating a problem. >> -Bob >> >> On 1/30/12 12:08 PM, Boel Brynedal wrote: >>> 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. >>> >>> ------------------------------------------------------------------------------ >>> Try before you buy = See our experts in action! >>> 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-dev2 >>> _______________________________________________ >>> svtoolkit-help mailing list >>> svt...@li... >>> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help >> >> ------------------------------------------------------------------------------ >> Try before you buy = See our experts in action! >> 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-dev2 >> _______________________________________________ >> svtoolkit-help mailing list >> svt...@li... >> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
