pmerge-list keeps failing on pvar (see error at bottom)

[Setss Provider]

i cannot figure out for the life of me why plink2 cannot generate pvar after the psam. 

i have confirmed that the various files i am merging have identical pvars.  i would have  imagined  it would only error when there  is a mismatch.  

initially, i had some strand mismatches, but i removed those SNPs and confirmed that all that was left matched precisely, but still no change  

i also checked to see if any of the CHR-BP combos weren't unique, but each SNP seems to have a unique address.

i actually have 52 studies to merge, but it does not work even if i limit it to a subset of these collections of pgen, pvar, and psam files.

 i would appreciate any guidance.

Thank you,

Caroline and Adi

PLINK v2.00a3.7 AVX2 (24 Oct 2022)

Options in effect:
  --make-pgen
  --out /gpfs/work5/0/pgcd0670/bicluster_followup/dir_ind_level_GWAS_links/dir_prscs/PGC4_bgs_int_sort_1-52_HRCEUR_200_0.5_allchr
  --pmerge-list /gpfs/work5/0/pgcd0670/bicluster_followup/dir_ind_level_GWAS_links/dir_prscs/study_PGC4_bgs_int_sort_1-52_HRCEUR_200_0.5_m05_path_and_stem_list.txt
  --threads 80

Hostname: tcn168.local.snellius.surf.nl
Working directory: /gpfs/scratch1/shared/arangan
Start time: Tue Jul 22 07:56:11 2025

Random number seed: 1753163771
257717 MiB RAM detected; reserving 128858 MiB for main workspace.
Using up to 80 threads (change this with --threads).
--pmerge-list: 5 filesets specified.
--pmerge-list: 17230 samples and 1 phenotype present.
--pmerge-list: Merged .psam written to
/gpfs/work5/0/pgcd0670/bicluster_followup/dir_ind_level_GWAS_links/dir_prscs/PGC4_bgs_int_sort_1-52_HRCEUR_200_0.5_allchr-merge.psam
.
--pmerge-list: 5 .pvar files scanned.
Error: Non-concatenating --pmerge-list is under development.

End time: Tue Jul 22 07:56:12 2025

[Setss Provider]

i reran it using the latest stable version of plink2. Same error. I also gave it a full node to make sure that the problem wasn't virtual memory or CPU limits.

PLINK v2.0.0-a.7LM 64-bit Intel (7 Jul 2025)       cog-genomics.org/plink/2.0/
(C) 2005-2025 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /gpfs/work5/0/pgcd0670/bicluster_followup/dir_ind_level_GWAS_links/dir_prscs/PGC4_bgs_int_snpmaf_1-52_HRCEUR_500_0.2_allchr.log.
Options in effect:
  --make-pgen
  --out /gpfs/work5/0/pgcd0670/bicluster_followup/dir_ind_level_GWAS_links/dir_prscs/PGC4_bgs_int_snpmaf_1-52_HRCEUR_500_0.2_allchr
  --pmerge-list /gpfs/work5/0/pgcd0670/bicluster_followup/dir_ind_level_GWAS_links/dir_prscs/study_PGC4_bgs_int_snpmaf_1-52_HRCEUR_500_0.2_path_and_stem_list.txt
  --threads 128

Start time: Tue Jul 22 18:19:30 2025
257716 MiB RAM detected, ~227003 available; reserving 128858 MiB for main
workspace.
Using up to 128 threads (change this with --threads).
--pmerge-list: 52 filesets specified.
--pmerge-list: 101533 samples and 1 phenotype present.

--pmerge-list: Merged .psam written to

/gpfs/work5/0/pgcd0670/bicluster_followup/dir_ind_level_GWAS_links/dir_prscs/PGC4_bgs_int_snpmaf_1-52_HRCEUR_500_0.2_allchr-merge.psam
.
--pmerge-list: 52 .pvar files scanned.
Error: Non-concatenating --pmerge[-list] is under development.
End time: Tue Jul 22 18:19:31 2025

JOB STATISTICS
==============
Job ID: 13255492
Cluster: snellius
User/Group: grouther/grouther
State: COMPLETED (exit code 0)
Nodes: 1
Cores per node: 128
CPU Utilized: 00:00:00
CPU Efficiency: 0.00% of 00:34:08 core-walltime
Job Wall-clock time: 00:00:16
Memory Utilized: 13.37 MB
Memory Efficiency: 0.01% of 224.00 GB (1.75 GB/core)

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[Chris Chang]

You are misunderstanding the error message.  “Concatenating” = “bcftools concat”, i.e. same samples DIFFERENT variants.

You should e.g. export to BCF and use “bcftools merge” if you’re dealing with nonoverlapping sample groups.

To view this discussion visit https://groups.google.com/d/msgid/plink2-users/CANj%3Dwf7i8_wYVYyj92rxQN6yOcbwgn4CdDfp4R135BftOhhd8g%40mail.gmail.com.

[Setss Provider]

Thank you. it also turned out that some of the files i was trying to merge were corrupted. i reexported them with the latest version of plink2 and was then able to merge them using the latest version of plink.

Thank you again