I am trying to run the
convertf tool in AdmixTools, as I have successfully run before. I am getting an error (warning perhaps? Because it appears to run to completion..?) that "snp order check fail; snp list not order". I built the original vcf file using GatherVCFs in GATK4 (previously CatVariants, GATK3), gathering the snp-called (HaplotypeCaller command) files in the order they were generated in, then used
vcftoolsto output ped/map format files.
convertf -p par.PED2EIGENSTRAT
Printed to screen:
parameter file: par.PED2EIGENSTRAT **warning: dubious parameter, please check the parameter name ## convertf version: 5000 genetic distance set from physical distance snp order check fail; snp list not ordered: p_subset_filteredSNPs_chr.map (processing continues) 23 1381 138077 zzz 509783 543784 snp order check fail; snp list not ordered: p_subset_filteredSNPs_chr.map (processing continues) 23 1381 138136 zzz 509784 543785 genotype file processed numvalidind: 35 maxmiss: 35001 eigenstrat output ##end of convertf run
I have not yet found a similar error online, and although convertf seems to finish, it does not produce a .geno file.
Any ideas on how to fix this issue would be greatly appreciated!
heys, I'm having a similar error, did you solve it?