Question: PLINK unable to read covariate file
0
zichunxu0824 • 0 wrote:
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!
ADD COMMENT
• link
•
modified 4 months ago
by
chrchang523 ♦ 7.1k
•
written
4 months ago by
zichunxu0824 • 0
Please use the formatting bar (especially the
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.