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
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.
Can you post the gender map file?
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.
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)?
Do you have two tabs on that line?
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.
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.
Bob Handsaker thank you very much, I think using the sample_gender.report.txt produced by preprocessing is the best option
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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