Segmentation Fault while dealing with LD

[Wang Zichong]

Hi, I am working on a Macbook Pro M4 24GB, macOS Sequoia 15.3.2. Recently I'm studying the usage of PLINK, and encounter segmentation fault running the official commands of tutorial. I'm sure I have done all previous procudure.

Following the last command of https://www.cog-genomics.org/plink/2.0/tutorials/qc2a, 

bogon:project1 zichong$ time plink2 \> --pfile ./data/processed/all_hg38_qcd \
> --make-pgen \
> --extract ./results/qc/qc3/all_hg38_qcd.prune.in  \
> --out ./data/processed/all_hg38_qcd_LE1
PLINK v2.0.0-a.6.10 M1 (11 Apr 2025)               cog-genomics.org/plink/2.0/
(C) 2005-2025 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to ./data/processed/all_hg38_qcd_LE1.log.
Options in effect:
  --extract ./results/qc/qc3/all_hg38_qcd.prune.in
  --make-pgen
  --out ./data/processed/all_hg38_qcd_LE1
  --pfile ./data/processed/all_hg38_qcd

Start time: Mon Apr 14 13:54:21 2025
24576 MiB RAM detected; reserving 12288 MiB for main workspace.
Using up to 10 threads (change this with --threads).
3202 samples (1603 females, 1599 males; 2583 founders) loaded from
./data/processed/all_hg38_qcd.psam.
6881079 variants loaded from ./data/processed/all_hg38_qcd.pvar.
2 categorical phenotypes loaded.
Segmentation fault: 11

real    0m7.668s
user    0m6.473s
sys     0m1.660s

I have tried version 6.19 M1 (29 Jan, 2025), but same problem. However, when I use a small subset (only Chr22) it worked, a bigger subset (only Chr1) the same error raised again. 

Thank you for your help!

[Christopher Chang]

Thanks for reporting this.  I've replicated the crash on my Mac; will try to post a bugfix later today.

[Christopher Chang]

Bugfix is now posted; let me know if you run into any more problems.

[Zichong Wang]

Thanks so much. It works well now.