Error: Segmentation fault (core dumped)

[chloe]

Hello,

I recently used PLINK2 to convert VCF files to PGEN format, using the following (which worked):
for CHR in `seq 1 22`

do 

plink2 --vcf vcf_file${CHR}.vcf.gz dosage=DS --id-delim _ --make-pgen --out out_file${CHR}

done

Following this, I wanted to merge the pgen files using:

plink2 --pmerge-list pgen_list_filenames.txt --make-pgen --debug --out merged_pgen

However, I receive an error message "Segmentation fault (core dumped) plink2 --pmerge-list pgen_list_filenames.txt --make-pgen --debug --out merged_pgen"

The output:

PLINK v2.00a4.5LM AVX2 AMD (13 Aug 2023) www.cog-genomics.org/plink/2.0/ (C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3

Logging to merged_pgen.log

Options in effect:

--debug

--make-pgen

--out merged_pgen

--pmerge-list pgen_list_filenames.txt

Start time: Thu Jul 17 07:44:12 2025

514860 MiB RAM detected, ~444985 available; reserving 257430 MiB for main workspace.

Using up to 4 compute threads.

--pmerge-list: 2 filesets specified.

--pmerge-list: 80654 samples present.

--pmerge-list: Merged .psam written to merged_pgen-merge.psam .

--pmerge-list: 2 .pvar files scanned, headers merged.

Concatenation job detected.

Concatenating... 0/1067198 variants complete. ^MConcatenating...10000/1067198 variants complete. ^MConcatenating...20000/1067198 variants complete. 

^MConcatenating...30000/1067198 variants complete. 

^MConcatenating...40000/1067198 variants complete. 

^MConcatenating...50000/1067198 variants complete. 

I ran this restricting to pgen files for only a couple of chromosomes (21-22), in case it could be due to insufficient memory or system resources. I also checked the pgen files and I don't see any clear issue with this. 

Please may I ask for your help with this - do you know why this could be happening (is it a memory/system resource issue or could it be something else)?

Thank you very much in advance.

Chloe

[Chris Chang]

Please retry with a newer PLINK2 build.

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[chloe]

Thank you very much - this now appears to be running.