my ($id, 
    $status, 
    $CDS_number, 
    $number_of_CDSs,
    $sequence_source,
    $startpos,
    $endpos,
    $startopen,
    $endopen,
    $complement) = $line =~ $long_regex; # Updated: Added ~

if ( $id =~ /\d{0,6}/ ) {
    print "ID:", $id, "appears to be valid\n";
    # Use $id...
}
...