Problem creating .bed files with plink

Question

[Loïs]

Hello everyone,

I'm having trouble creating a bed file with plink.

Here is what my .ped file looks like:

# Stacks v2.61;  PLINK v1.07; July 02, 2023
Fos_ext XY1     0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Fos_ext XY2     0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Fos_ext XY3     0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Fos_ext XY4     0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Fos_ext XY5     0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Lyon_StEx_ext   XY7     0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Lyon_StEx_ext   XY8     0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Lyon_StEx_ext   XY10    0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Foret_Menton    XY11    0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 >
Foret_Menton    XY12    0       0       0       0       G       G       G       G       C       C       T       T       T       T       A       G       0       0       A       A       G       G       A >
Foret_Menton    XY13    0       0       0       0       G       G       G       G       C       C       T       T       T       T       G       G       G       G       A       A       G       G       0 >

The command I use :

plink --file populations.plink --make-bed --out populations.plink --allow-no-sex --allow-extra-chr --no-sex --no-parents --no-fid --no-pheno

and the error message I get :

PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to populations.plink.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --file populations.plink
  --make-bed
  --no-fid
  --no-parents
  --no-pheno
  --no-sex
  --out populations.plink

31701 MB RAM detected; reserving 15850 MB for main workspace.
Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.
Rescanning .ped file... 0%
Error: Half-missing call in .ped file at variant 1, line 2.

Any idea where the problem might be coming from and how to solve it?

thanks