segmentation fault on --pmerge-list

[Grant Billings]

I imported VCF files generated from GATK pipeline (HaplotypeCaller -> GenomicsDBImport -> GenotypeGVCFs) for 26 separate chromosomes (cotton) into separate .pgen+.bim+.fam file sets with the following command (output from one chromosome shown:

for f in *.vcf.gz; do chr=$(basename $f .vcf.gz); echo "$chr"; ./plink2 --make-bpgen --vcf "$chr".vcf.gz --vcf-min-dp 5 --vcf-max-dp 500 --allow-extra-chr --max-alleles 2 --set-all-var-ids @_# --out "$chr" --maf 0.01 --geno 0.90; done

PLINK v2.00a3LM AVX2 Intel (29 Jan 2022)       www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to A01.log.
Options in effect:
  --allow-extra-chr
  --geno 0.90
  --maf 0.01
  --make-bpgen
  --max-alleles 2
  --out A01
  --set-all-var-ids @_#
  --vcf A01.vcf.gz
  --vcf-max-dp 500
  --vcf-min-dp 5

Start time: Thu Feb 17 13:04:39 2022
32110 MiB RAM detected; reserving 16055 MiB for main workspace.
Using up to 10 threads (change this with --threads).
--vcf: 1569297 variants scanned.
--vcf: A01-temporary.pgen + A01-temporary.pvar.zst + A01-temporary.psam
written.
173 samples (0 females, 0 males, 173 ambiguous; 173 founders) loaded from
A01-temporary.psam.
1536155 out of 1569297 variants loaded from A01-temporary.pvar.zst.
Note: No phenotype data present.
Calculating allele frequencies... done.
--geno: 31920 variants removed due to missing genotype data.
764964 variants removed due to allele frequency threshold(s)
(--maf/--max-maf/--mac/--max-mac).
739271 variants remaining after main filters.
Writing A01.fam ... done.
Writing A01.bim ... done.
Writing A01.pgen ... done.
End time: Thu Feb 17 13:05:03 2022

Then made my mergelist and tried to import into  new fileset:

for i in *.pgen; do echo $(basename "$i" .pgen) >> mergelist.txt; done

cat mergelist.txt

A01
A02
A03
A04
A05
A06
A07
A08
A09
A10
A11
A12
A13
D01
D02
D03
D04
D05
D06
D07
D08
D09
D10
D11
D12
D13

./plink2 --allow-extra-chr --make-bpgen --pmerge-list mergelist.txt bpfile --out AllChr

PLINK v2.00a3LM AVX2 Intel (29 Jan 2022)       www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to AllChr.log.
Options in effect:
  --allow-extra-chr
  --make-bpgen
  --out AllChr
  --pmerge-list mergelist.txt bpfile

Start time: Thu Feb 17 13:05:46 2022
32110 MiB RAM detected; reserving 16055 MiB for main workspace.
Using up to 10 threads (change this with --threads).
--pmerge-list: 26 filesets specified.
--pmerge-list: 173 samples and 1 phenotype present.
--pmerge-list: Merged .psam written to AllChr-merge.psam .
Segmentation fault

Any ideas? Happy to share input data if it would help. Not sure why it's saying I have a phenotype present (I didn't have any to begin with).  Each of the original input VCF files has the same individuals (173).

Grant

[Christopher Chang]

Yes, if you could send me a set of files (could be two instead of 26 filesets) that I could reproduce the segfault with, that would be very helpful.

[Grant Billings]

I sent a private message to you with the fileset that gave me the segfault. Let me know if you need anything else.

[Christopher Chang]

Thanks, bugfix (for mishandling of extra chromosome names in --pmerge) is posted.

[Grant Billings]

My merge succeeded with the new version. Thank you!!!