This is in the original script as well, but since this version is prettier to look at, I'll comment here.

sub parseFile {
    my ($fIn) = @_; # a filehandle
    my $fastaData;

    ... #yada yada yada

    while (<$fIn>) { # $/ has not been undefined, $fIn is read line by
+ line
        $fastaData = $_;
        $fastaData =~ s/\n//gms; #/gms are all useless because:
                                 #g - each time $fastaData will have e
+xactly one \n (at the end)
                                 #m - regex doesn't use ^ or $, and it
+'s always a single line anyways
                                 #s - regex doesn't use . and it's alw
+ays a single line anyways
            # effectively performs the same function as
        # chomp($fastaData);
            # or even
        # chomp($fastaData = $_);

        ...
    }
    ...
}
[download]

Has nothing to do with the error but if we're on the subject of cleaning up the code, this is something that made me do a double-take.

On a less related note, GMS is also the name of a Dutch trance duo, whose three-hour live performance at a festival I attended was a life-changing experience, which is why that particular combination of letters always brings back the good vibes :^)