PLINK error: no --covar values loaded
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6.2 years ago
kindlychung ▴ 60

Here is the command that I used:

plink --allow-no-sex --bfile ./collr_task_Curliness-sex_age_s400_p1.00e-01/RS123_3069obs_shift_0000 --covar curliness_RS_withIID.tab --covar-name sex,age --linear hide-covar --out ./collr_task_Curliness-sex_age_s400_p1.00e-01/RS123_3069obs_shift_0000 --pheno curliness_RS_withIID.tab --pheno-name Curliness

And here is the log:

PLINK v1.90b2m 64-bit (15 Oct 2014)        https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to ./collr_task_Curliness-sex_age_s400_p1.00e-01/RS123_3069obs_shift_0000.log.
96680 MB RAM detected; reserving 48340 MB for main workspace.
831138 variants loaded from .bim file.
2905 people (0 males, 0 females, 2905 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
./collr_task_Curliness-sex_age_s400_p1.00e-01/RS123_3069obs_shift_0000.nosex .
2221 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Error: No --covar values loaded.

Note that I used the same file for --pheno and --covar, but plink didn't complain about --pheno at all.

The first 3 lines of the phenotype file looks like this:

FID IID ImageID Curliness sex age ergoid
1b 42326 102347101654 NA m 68.7527777777778 82002
1a 2112329 773125453 0 m 69.2194444444444 261001
plink gwas • 4.2k views
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The first thing I'd check is the capitalization of "sex" and "age" in your phenotype file.

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They are both lower case, I have checked.

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1
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Oh, the actual problem is that sex is not a numeric covariate.  This should work after you recode it to e.g. 1 = male, 2 = female.

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Oh, my bad. I should have spotted this right away. Thanks! Could you put this into an answer so that I can accept it?

 

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6.2 years ago

--covar requires numeric phenotypes.  Representing sex as 1 = male and 2 = female, instead of m = male and f = female, should work.

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