SAIGE GWAS - error - samples in geno file do not have phenotypes

Question

[Nance]

Hey, so I have this error when running step 1 of saige with a subset of my plink files, and pheno file, following the tutorial from https://github.com/weizhouUMICH/SAIGE/

Error::

5685 samples in geno file do not have phenotypes

0 samples will be used for analysis

But as confirmed in R, there is large overlap between these files and should be around ~3000 samples. The error remains the same when I dos2unix, keep only one fid/iid column, remove missing data, or use a different phenotype.

Is there another reason I could be getting this error / the ID isn't parsing correctly between the files when using saige? Has anyone else had a similar error from another reason?

Thanks!