[svtoolkit-help] SVDiscovery: No gender data

[Margarida C. M. <mm...@co...>]

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)