Plink1.07 generate ERRORs when reading covaries

Question

[heqianchange]

Hi, everyone.

I am using Plink1.07 to do GWAS. When I go to logistic association analysis with covaries will generate errors. I make the covariate files using a text editor. I also check the format of covariate files but failed to find the problem. Can some expert help me?

It works well when use --logistic independently.

================================================================
Options in effect:
    --bfile whi_garnet_update_12
    --covar co_var_garnet_test0305.txt
    --covar-name BMIX
    --logistic
    --hide-covar
    --out logistic_results_0305
    --noweb

Reading map (extended format) from [ whi_garnet_update_12.bim ] 
4097793 markers to be included from [ whi_garnet_update_12.bim ]
Reading pedigree information from [ whi_garnet_update_12.fam ] 
4686 individuals read from [ whi_garnet_update_12.fam ] 
2539 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
185 cases, 2354 controls and 2147 missing
0 males, 4686 females, and 0 of unspecified sex
Reading genotype bitfile from [ whi_garnet_update_12.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Line:
D100015-30  D100015-30          28.91999043786982
ERROR: Problem reading the covariates
==========================================================
The format of the covariable file is: FID IID BMIX without missing values.

Answer 1

[zx8754]

Ensure your covar file is per expected format, I can see 3 tabs after the second column, meaning plink thinks there are 5 columns not 3, and column 3, 4 becomes missing, hence the error.

[heqianchange]

Thank you very much. I revised the format of the covariable file and the error has gone.