Re: [svtoolkit-help] SVDiscovery: No gender data

[Bob H. <han...@br...>]

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)
>
>
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