Try this, it should be faster. But I'm sure it could be improved further...

open (INFILE, $ARGV[0]) or die "unable to open file: $!";
# It's a good idea to check the error message in Perl's special variab
+le $!
my ($a_count, $c_count, $g_count, $t_count, $err_count) = 0;
while ( <INFILE> ) {
   s/^>genome//;
   s/\s//g;
   $a_count   += tr /[Aa]//;
   $c_count   += tr /[Cc]//;
   $g_count   += tr /[Gg]//;
   $t_count   += tr /[Tt]//;
   $err_count += tr /[ACGTacgt]//c;
}
print "As: $a_count\n",
      "Cs: $c_count\n",
      "Gs: $g_count\n",
      "Ts: $t_count\n",
      "Errors: $err_count\n";
[download]

hth

dave