--set-all-var-ids cant distinguish chr in PLINK v2.00a3 AVX2 (15 Mar 2022)

[Jard de Vries]

Dear all,

I am using PLINK v2.00a3 AVX2 (15 Mar 2022) and want to change the variant names to chr:pos:ref:alt , but everytime I try a variation of --set-all-var-ids @:# or --set-all-var-ids @:#:$r:$a it will give the error message:

Error: Variant names are limited to 16000 characters.

Full command:

plink2 --bfile data1 --set-all-var-ids @:#:\$r:\$a --make-bed --out data2

It also doesnt matter if I use pfam or bed input.

I know that I was able to normally use --set-all-var-ids on this server before, but after the update of the plink version, I am no longer able to. 

On a different server, we still have PLINK v2.00a3LM 64-bit Intel (25 May 2021)

and there the command still works as normal. For the time being, we run this step on this server.

Is this a known bug? Does it expect certain characters around the chr and pos in the plink files?

Thanks for any help!

[Christopher Chang]

Hmm, there was an AVX2-specific bugfix in May, though I wasn't aware of it affecting this function.  Can you try rerunning with the current build, and if it fails, post the full .log file and ideally also a .bim (could contain just one variant) that lets me reproduce the issue?

[Jard de Vries]

I have added a "head data1.bim" from both servers as attachment. 

Full command + log:

--------------------------------------

plink2 --bfile data1 --set-all-var-ids @:#:\$r:\$a --make-bed --out data2

PLINK v2.00a3 AVX2 (15 Mar 2022)               www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to data2.log.
Options in effect:
  --bfile data1
  --make-bed
  --out data2

  --set-all-var-ids @:#:$r:$a

Start time: Sun Aug 14 15:40:27 2022
257858 MiB RAM detected; reserving 128929 MiB for main workspace.
Using up to 48 threads (change this with --threads).
24 samples (0 females, 0 males, 24 ambiguous; 24 founders) loaded from
data1.fam.

Error: Variant names are limited to 16000 characters.

End time: Sun Aug 14 15:40:27 2022

----------------------------------

Should I ask our Server management to downgrade to the previous version to see if that solves the problem?

Kind regards,

Jard

Op donderdag 11 augustus 2022 om 15:17:43 UTC+2 schreef chrch...@gmail.com:

[Christopher Chang]

Ok, I've replicated the issue with this .bim, and it still exists in the current build.  I will post a bugfix today.

[Christopher Chang]

Bugfix is posted.