plink sex check error

[Rabu]

Hi everyone,
I am using plink sex check on my sequenced samples, but after I run:
plink --bfile example --check-sex the plink.sexcheck file contains no value under the F column, it just says "nan", does anyone know what the issue is? I have all my binary files (example.fam, example.bim, example.bed), so I don't know where I am going wrong.

Thanks in advance

[Rabu]

Hi again, so I managed you get all the F values, but a lot of the sample sexes aren't matching up with the SNP sexes.

Could this be because my vcf files contain no homozygous reference calls? They only contain homozygous alternate and heterozygous calls. Would this skew the sex check data?

Thanks again