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Contamination test, Error in dimnames(x) #615

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asli1-han opened this issue Feb 21, 2024 · 0 comments
Open

Contamination test, Error in dimnames(x) #615

asli1-han opened this issue Feb 21, 2024 · 0 comments

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@asli1-han
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Hi, I am currently working on ANGSD contamination test. I installed angsd0.938 master file and using this code:

Rscript angsd/R/contamination.R mapFile="angsd/RES/chrX.unique.gz" hapFile="angsd/RES/HapMapChrX.gz" countFile="project.bam.icnts.gz" mc.cores=24 > project.outR

and I am receiving this error:
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
Calls: doAnal -> mismatch -> colnames<-
Execution halted

I checked the chrX.unique.gz and HapMapChrX.gz files and they have different structures, probably they are the reason. How can I find the right version of the files or should I change the code itself?

Thank you!

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