When using the .faa file, there is a prompt indicating that there are invalid residues.

[704913307]

FASTA-Reader: Ignoring invalid residues at position(s): On line 33162: 5, 7, 9, 11-13, 18, 22-23, 25-26, 32, 38, 47-49, 51-53, 58
FASTA-Reader: Ignoring invalid residues at position(s): On line 33163: 1, 3-4, 6, 8-9, 16-17, 19, 24, 27, 29-30, 32, 36-37, 40, 43-44, 52-53
FASTA-Reader: Ignoring invalid residues at position(s): On line 33164: 3-5, 8, 10-11, 25, 27-28, 31
Found 0 genes in assembly13clean.fa.faa
Tip: found a bug in abricate? Post it at https://github.com/tseemann/abricate/issues.
Done.