while (<$fh1>) { # Reading first hash
    my ($id, undef, undef, undef, $seq) = split;
    if ( exists $bow1{$ID} ){
       warn "ID \'$id\' already exists for hash 1!\nThe current sequence value is \'$bow1{$id}\', which would be replaced with \'$seq\'.\n";
       .... handle the error better (maybe ignore if sequences are the same?) ....
       next; ## skip it
    }
    $bow1{$id} = $seq;
}
close $fh1 || die "Failed to close $file1 : $!";