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Segmentation fault PLINK 1.90b

Hello everyone,

I am using this line to make my .ped .bed/etc files for PLINK (--version, 1.90b) to run some genetic analyses.

This line works perfectly:

plink --nonfounders --allow-no-sex  --lfile final_report_sheep --missing-genotype - --output-missing-genotype 0 --recode --allow-extra-chr --chr-set 26 --out Sheep

However, when I add --autosome, it gives me a "segmentation fault". Same thing when I tried --chr 1-26 or --no-chr X, Y, mt .

Anyone that might now if it is something I am mis-specifying or the issue is with the version I am using?

Thanks in advance!

Best, Alex

plink
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updated by chrchang523 chrchang523 • written by Alexandros.Frydas • Alexandros.Frydas

What is the output of “plink —version”?

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written by chrchang523 chrchang523

Hello,

Thanks for the reply.

The output is:

PLINK v1.90b6.21 64-bit (19 Oct 2020)

I ended up re-making my .fam, .lgen and .map files to override this, excluding all variants from non-autosomal, so it is fine now for me. Now there is a new struggle with the --pheno command, but I am still working on that before coming here.

Thanks, Alex

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written by Alexandros.Frydas • Alexandros.Frydas

I am unable to reproduce your initial segmentation fault, which should be fixed on my end. Can you please add --debug and then post full .log output from a segfaulting run? (A matched .log from the preceding successful run without —autosome would also be helpful.)

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written by chrchang523 chrchang523

Hello,

Sorry for the delayed response, I was able to proceed much further in my analysis, thankfully :)

If it is still helpfull for you, I will try to relocate the files and re-run the problematic line with --debug and get back on you with the log report by tomorrow!

Thanks, Alex

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written by Alexandros.Frydas • Alexandros.Frydas

Yes, that would be helpful.

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written by chrchang523 chrchang523

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