Plink2 Segmentation fault upon --make-pgen when --removing or --keep flag is utalized

[Lucas Fishbein]

I am working on a linux system and when I input the command: 

"plink2 --pfile M85_unique --make-pgen -out M85_no_outliers"

I have no issues, but when I do attempt to remove a few cases via the --remove flag I get a Segmentation fault during the .pgen writing process, shown below:

plink2 --pfile M85_unique --remove outlier_lists/final_exclusions.txt --out M85_no_outliers --make-pgen

PLINK v2.00a6LM 64-bit Intel (4 Jul 2024)      www.cog-genomics.org/plink/2.0/

(C) 2005-2024 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to M85_no_outliers.log.

Options in effect:

  --make-pgen

  --out M85_no_outliers

  --pfile M85_unique

  --remove outlier_lists/final_exclusions.txt

Start time: Fri Jul 19 14:59:09 2024

1031255 MiB RAM detected, ~967608 available; reserving 515627 MiB for main

workspace.

Using up to 9 threads (change this with --threads).

85 samples (47 females, 38 males; 85 founders) loaded from M85_unique.psam.

19793077 variants loaded from M85_unique.pvar.

Note: No phenotype data present.

--remove: 82 samples remaining.

82 samples (45 females, 37 males; 82 founders) remaining after main filters.

Writing M85_no_outliers.psam ... done.

Writing M85_no_outliers.pvar ... 94%^done.

Writing M85_no_outliers.pgen ... 0%Segmentation fault (core dumped)

This leaves an empty .log file and a .pgen file with issues. 

My final_exclusions.txt has just one column and three case IDs:

#IID

IID1

IID2

IID3

IID4

IID5

IID6

I have tried using --keep but get the same issue, I have also tried removing a variety of the IDs from the exclusion list but found the process only runs successfully when there are no IDs in the exclusion list.

Do you have any insights into this problem?

[Lucas Fishbein]

I got past this error by changing my Plink2 version to the Alpha 5.12 final

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[Christopher Chang]

Interesting.  So this is a bug introduced in alpha 6.

Is there a dataset you can post that I can use to replicate the segfault?  (Ok to e.g. first filter out everything past chr1, if the segfault then still occurs.)

If not, what is the output of "plink2 --pfile M85_unique --pgen-info"?  Is it possible for you to run a sequence of debug builds?