Hello everyone, I am doing a GWAS analysis by plink 1.9. When I upload my covariate file, it reads
Ignoring --covar since no commands reference the covariates
I have double-checked my covariate file and it is in the right format (as it works as a phenotype file). I have also checked the value of the covariate file (with R) and it is indeed numeric. Here it is my command:
--bfile ../genotype_all/qc_1 --pheno ../phenotype/weight --covar test_covar.txt --covar-number 1 --assoc
and here it is the log:
Logging to plink.log. Options in effect: --assoc --bfile ../genotype_all/qc_1 --covar test_covar.txt --covar-number 1 --pheno ../phenotype/weight 64266 MB RAM detected; reserving 32133 MB for main workspace. 449792 variants loaded from .bim file. 488371 people (223470 males, 264803 females, 98 ambiguous) loaded from .fam. Ambiguous sex IDs written to plink.nosex . 486613 phenotype values present after --pheno. Using 1 thread (no multithreaded calculations invoked). Warning: Ignoring --covar since no commands reference the covariates.
Can anyone tell what is wrong? Thank you very much for your help!