Plink –merge-list only outputting fam

I am attempting to merge Plink files towards an algorithm I am using (CookHLA). I have already made the bed/bim/fam files for my vcf files. Now, I want to merge them into a single file so I can progress with the algorithm.

To do this, I am running the following line of code:

plink --bfile 0002 --merge-list PLINK_UniqueNames --make-bed --threads 4 --out Merged_Plink_files

0002 refers to the first set of plink out (I am unsure what to use as a reference). I am getting lots of warnings about non ATGC variants, ie ‘.’.

My issue is that only a fam file is outputted when I need the full set. I was hoping for some assistance. I admittedly do not have much experience with Plink so any assistance would be appreciated.

Contents of the fam file (just a few lines):

0002    0002    0   0   0   -9
0005    0005    0   0   0   -9
0007    0007    0   0   0   -9
0008    0008    0   0   0   -9
0009    0009    0   0   0   -9
001 001 0   0   0   -9