I'm using plink 1.9 and running the command:
plink --bfile data --genome --extract data.prune.in --remove data.fail_imiss where data.fail_imiss is a file with individuals with proportions of missing SNPs greater than greater than the threshold .05 . I get the warnings: Warning: 10745 het. haploid genotypes present (see plink.hh ); many commands treat these as missing. Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands treat these as missing.
followed by the error message:
Error: Pedigree graph is cyclic. Check for evidence of time travel abuse in your cohort.
I have never seen this error message before and I was wondering if anyone could help me figure it out.