#!??? How does one leave "something out from the copy and paste?" :-)

No syntax errors found. Warnings in OP appear to come from Bio:xxx; not from Perl.

Based on the warning MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?] and the fact I can't find any attempt in your code to "validate" a "$seq" with such a character class nor even a ($temp_seq I have to wonder: could your fastaTestData.fna be corrupt?

Fixed unclosed code tag