I am trying to run a GWAS with a quantitative phenotype in PLINK. I'm using linear regression with principal components from population structure analysis as covariates. The command is as follows:
plink --bfile genotypefile --pheno pheno.txt --allow-no-sex --covar covariates --covar-name PC1,PC2,PC3,PC4 --out gwas_results --linear hide-covar --adjust
The log file says that there are 0 phenotype values present after --pheno and I have received the following error:
--linear without --all-pheno requires a scalar phenotype
I am not sure how this could be because my phenotype is scalar and I have conducted GWAS with this same sample and a very similar phenotype with the same file format without issue. The phenotype file is in a .txt document that looks like this:
FID IID pheno 0002 0002 10.18651 0005 0005 31.99052 0007 0007 44.79303 0081 0081 39.33981 0082 0082 -15.43773 0083 0083 31.8429 0088 0088 -18.39446
I'm not sure what I can do to resolve this issue. Any input would be greatly appreciated.