I am trying to include the --keep and --remove options in my plink2 command. I am finding that despite my files for these options having identical text to the main file's IDs, all the samples are removed.

    Command: plink2 --bfile  pca_final --keep EUR.sample --remove toberemoved.txt \
    --make-bed --out unrelated_EUR


So my original .fam file has: 

    0002

The --keep file would have:

    #FID	IID
    0002	0002

The --remove file would have:

    #FID	IID
    1067	1067



I was able to figure out the issue. The FID column (the first column in the fam file) was all zeroes and I put text there as I was confused by the format used by my colleague.