GenomeSTRiP analysis error
If you are seeing an error, please provide(REQUIRED) :
a) GenomeSTRiP version 2.00.1958
##### ERROR stack trace
org.broadinstitute.sv.commandline.ArgumentException: Unrecognized gender for sample ERR123456: ERR123456
at org.broadinstitute.sv.metadata.gender.GenderMap.readGenderMapFile(GenderMap.java:105)
at org.broadinstitute.sv.metadata.gender.GenderMap.init(GenderMap.java:56)
at org.broadinstitute.sv.metadata.gender.GenderMap.<init>(GenderMap.java:42)
at org.broadinstitute.sv.metadata.gender.GenderMap.open(GenderMap.java:38)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initMetaData(SVDiscoveryWalker.java:194)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:79)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:145)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:95)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
I have been trying to run an analysis on my samples but I keep getting the above-mentioned error. The preprocessing step runs without giving an error but the SV discovery gives this error. I have checked the gender.map and everything is written correctly, after receiving this error I have re-run the script 3 more times, but still, I get this error. I don't know what the problem could be.
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Can you post the gender map file?
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The issue is with the highlighted sample (ERR1955423). I have attached an image of the gender map file. and also posted a part of the file. I'm doing an analysis of over 200 samples.
190618_FD09251561 M
190618_FD09251568 F
190618_FD09251569 F
ERR1955423 F
ERR1955529 M
ERR1955524 M
ERR1955438 F
ERR1955419 F
ERR1955398 M
ERR1955487 M
ERR1955462 F
ERR1955431 F
ERR1955515 M
ERR1955528 F
ERR1955413 M
ERR1955481 F
ERR1955427 M
ERR1955461 F
ERR1955397 M
ERR1955482 M
ERR1955432 F
ERR1955464 M
ERR1955457 F
ERR1955477 M
ERR1955470 F
ERR1955538 M
ERR1955469 F
ERR1955430 M
ERR1955493 F
ERR1955460 M
ERR1955534 F
ERR1955420 M
ERR1955443 F
ERR1955406 M
ERR1955527 F
ERR1955429 M
ERR1955425 F
ERR1955463 M
ERR1955516 M
ERR1955451 M
ERR1955526 F
ERR1955476 M
ERR1955512 F
ERR1955513 M
ERR1955488 F
ERR1955412 M
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Is there some reason you are not using the file produced by preprocessing (sample_gender.report.txt)? This is what will be used by default if you do not supply your own gender file.
Does your have a header (which for a two-column file must be SAMPLE GENDER)?
Are the line terminators correct (Unix style)?
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Do you have two tabs on that line?
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I did not have any specific reason, I think the best way would be to use the sample_gender.report.txt because I thought its a requirement to have a gender map file.
It does not have a header, its a Unix style, it has two tabs the one with the sample and another with the gender.
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If you are going to supply your own, it needs to have a header, it should be tab-delimited.
If it is a two column file, each line should have one tab. I suspect that the line where you are getting an error has two tabs (i.e. three columns) and the second column is empty.
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Bob Handsaker thank you very much, I think using the sample_gender.report.txt produced by preprocessing is the best option
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It's usually best, unless you think it is wrong for some reason (due to a really unusual aneuploidy on the sex chromosomes or something like that).
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