-check-sex/--impute-sex requires at least one polymorphic X chromosome locus

[Osama Aziz]

 I keep encountering the same message when I try to go through with my sex check. I've done the SNP missingness step, it's this step that keeps stumping me. In my data, I have only 22 chromosomes.

F:\GWAS>plink --bfile filtered_genotype_data4 --check-sex
PLINK v1.90b7.2 64-bit (11 Dec 2023)           www.cog-genomics.org/plink/1.9/
(C) 2005-2023 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.log.
Options in effect:
  --bfile filtered_genotype_data4
  --check-sex

32392 MB RAM detected; reserving 16196 MB for main workspace.
9555220 variants loaded from .bim file.
127937 people (46175 males, 81762 females) loaded from .fam.
127937 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 127937 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.996433.
9555220 variants and 127937 people pass filters and QC.
Among remaining phenotypes, 6581 are cases and 121356 are controls.
Error: --check-sex/--impute-sex requires at least one polymorphic X chromosome
locus.

[Christopher Chang]

I am not sure why you are expecting --check-sex to work when you have no sex-chromosome data.