I was sent a .bed file with the corresponding .fam and .bim files to run in terminal using ADMIXTURE. Initially, when running Admixture on the .bed file, it would fail and the error said "PLINK Input file error". I tried to work around using the shared files and instead created a .ped and .map file. When trying to run Admixture on the .ped file produced the same error "PLINK Input file error", I tried running the original .bed file again which gave a different error code "Error: detected that all genotypes are missing for a SNP locus. Please apply quality-control filters to remove such loci." I ran ADMIXTURE on a sample .bed file to make sure there was not an issue with the program and that produced the expected output when using Admixture, so I know it is a problem with my files, but I cannot figure out what.
When I tried converting the .bed file into .ped and .map, I was able to successfully using PLINK. However, these files will not run with ADMIXTURE. I then tried creating practice .ped/.map files with only 6 rows of my data to see if I could get the format correct first. I did this using vim in terminal. Screenshot of .ped file created with vim in terminal Screenshot of .map file created with vim in terminal
When I attempt to run admixture on this new .ped file, it also errors "PLINK Input file error"
brigettewaldrup@C02X28CRJG5L ringman % ./admixture practice_ringman_pedfile.ped 3
**** ADMIXTURE Version 1.3.0 ****
**** Copyright 2008-2015 ****
**** David Alexander, Suyash Shringarpure, ****
**** John Novembre, Ken Lange ****
**** ****
**** Please cite our paper! ****
**** Information at www.genetics.ucla.edu/software/admixture ****
Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
PLINK Input file error
I went back to the original .bed file and tried running ADMIXTURE again and this is when I received a different error code "Error: detected that all genotypes are missing for a SNP locus. Please apply quality-control filters to remove such loci."
brigettewaldrup@C02X28CRJG5L ringman % ./admixture RINGMAN_n66_preQC_2023Mar21.bed 3
**** ADMIXTURE Version 1.3.0 ****
**** Copyright 2008-2015 ****
**** David Alexander, Suyash Shringarpure, ****
**** John Novembre, Ken Lange ****
**** ****
**** Please cite our paper! ****
**** Information at www.genetics.ucla.edu/software/admixture ****
Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
Error: detected that all genotypes are missing for a SNP locus.
Please apply quality-control filters to remove such loci.
Here is a screenshot of my .fam/.bim/.bed files opened to get an idea of the data: Screenshot of .fam/.bim/.bed files
I apologize if any of my vocabulary is incorrect, I am new to all of this and would appreciate any and all help!