Re: [svtoolkit-help] SVDiscovery: No gender data
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Re: [svtoolkit-help] SVDiscovery: No gender data
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From: Margarida C. M. <mm...@co...> - 2012-07-31 19:32:51
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Thank you Rob and Ashish for the advice. I will run SVDiscovery without the gender file for the autosomes and then check the sample ids for the X chromosome. Margarida On Jul 31, 2012, at 12:32 PM, Ashish Kumar wrote: > I guess I have seen this before. > Quick and easy solution, if you are doing this only for autosomes, then remove the option "-genderMapFile" and you get rid of the problem for now. > > For resolving this, please make sure your gender mapfile has same sample ids as reflected in the BAM headers of each BAM. > > Best, > Ashish > > ________________________________________ > From: Bob Handsaker [han...@br...] > Sent: 31 July 2012 17:25 > To: svt...@li... > Subject: Re: [svtoolkit-help] SVDiscovery: No gender data > > I'd check the basics: > - make sure the gender file is tab-delimited > - make sure the gender file is specified on the command line > - make sure there's nothing funny about the line endings (e.g. use "file > your-gender-file" on unix) > You don't need to re-preprocess to run a subset of samples, you can just > drop the relevant bam files. > If after checking this you can't find it, you can try sending me the > complete log file for the failing run and the gender file you are using. > -Bob > > On 7/31/12 12:15 PM, Margarida Cardoso Moreira wrote: >> Dear Bob Handsaker, >> >> I am getting an error that I cannot completely understand while running SVDiscover: "No gender data for sample: A11111". >> >> I checked the gender file and the line of text referring to that genome is equal to the other lines. Genome's Strip metadata doesn't show any abnormality with that sample. I ran SVDiscovery again after removing that sample (having ran first SVPreprocess without that sample) and I got the same error but now for a different sample. I am working with ~900 bam files and these 2 are in the middle of the bam list file. >> >> I don't understand what could be wrong with the gender file to produce such an error. >> >> Thank you for your help, >> >> Margarida >> >> ##### ERROR ------------------------------------------------------------------------------------------ >> ##### ERROR stack trace >> java.lang.RuntimeException: No gender data for sample: A11111 >> at org.broadinstitute.sv.discovery.ClusterMembershipModule.init(ClusterMembershipModule.java:182) >> at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.createMembershipModule(DeletionDiscoveryAlgorithm.java:1062) >> at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.initClusterModules(DeletionDiscoveryAlgorithm.java:1007) >> at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:317) >> at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:191) >> at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:168) >> at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45) >> at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) >> at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:76) >> at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234) >> at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) >> at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105) >> at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) >> at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67) >> at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) >> ##### ERROR ------------------------------------------------------------------------------------------ >> ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): >> ##### ERROR >> ##### ERROR Please visit the wiki to see if this is a known problem >> ##### ERROR If not, please post the error, with stack trace, to the GATK forum >> ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki >> ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa >> ##### ERROR >> ##### ERROR MESSAGE: No gender data for sample: A11111 >> ##### ERROR ------------------------------------------------------------------------------------------ >> >> at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) >> at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) >> at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) >> at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) >> at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) >> at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) >> at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) >> at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) >> at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> svtoolkit-help mailing list >> svt...@li... >> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
