Problem using covariate file

[ch...@cornell.edu]

Hi,

I am trying to run a logistic regression with covariates included in the model. I am running the following command:

 plink --ped file.plk.ped --map file.plk.map --allow-extra-chr  --no-parents --no-sex --allow-no-sex --no-fid --covar cov.plk --logistic

This is the output:

Random number seed: 1501684755
64356 MB RAM detected; reserving 32178 MB for main workspace.
Scanning .ped file... done.
Performing single-pass .bed write (4621 variants, 145 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
4621 variants loaded from .bim file.
145 people (0 males, 0 females, 145 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
144 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
--covar: 1 covariate loaded.
145 people were not seen in the covariate file.
Before main variant filters, 145 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.9289.
4621 variants and 145 people pass filters and QC.
Among remaining phenotypes, 61 are cases and 83 are controls.  (1 phenotype is
missing.)
Warning: Skipping --logistic since # variables >= # samples.
(Check your covariates--all samples with at least one missing covariate are
excluded from this analysis.)

End time: Wed Aug  2 10:39:15 2017

I have attached truncated versions of my .ped and cov.plk file. I believe they are both formatted correctly. Any insight into what is going on would be greatly appreciated.

Thanks,

Chris

[Christopher Chang]

The issue is that the --no-fid flag only applies to .fam/.ped files; it is not applied to anything else.  You'll need to duplicate the first column of your covariate file; sorry about the inconvenience.

[ch...@cornell.edu]

I duplicated the column and it worked. Thanks for your help.