PLINK1.9 Segmentation fault (core dumped)

Question

[krishii]

Hi,

I am trying to create .bim/fam and bed files from map and ped files. But I got different error messages and I sorted out those with the below code. However, I was not able to create the above file. Kindly help me in this regard.

plink1.9 --file UK-3121_220411_PLINK_PCF_TOP --make-bed --chr-set 26 no-xy no-mt --allow-extra-chr --allow-no-sex --nonfounders --out UK

16106 MB RAM detected; reserving 8053 MB for main workspace. Segmentation fault (core dumped)

Thank you.

[chrchang523]

On the plink2-users Google group, I asked you to provide at least the plink 1.9 version string, which you inexplicably omitted from the output you copied.

[LauferVA]

while i hesitate before commenting on a thread relating to plink2 that has already been addressed by literally chris 'no, seriously' chang, in my experience this kind of thing is typically misspecified input. also, provide the bit of output hes asking for, it will help you.

Answer 1

[M.O.L.S]

Perhaps just use --make bed and stop there.

Answer 2

[chrchang523]

For the record, the segmentation fault was due to a bug that was fixed on 28 Apr 2020; there should have been an error message reporting that the input file had chrX/chrY/chrM, in violation of the specified chromosome set.

The correct flag for filtering out chrX/chrY/chrM, when they are in the input, is “—not-chr X Y MT”.