my $file = "project.txt";
# Use three-argument form of open() (available in perl 5.6.0) 
# and check the return value.
open(FILE, '<', $project) or die "Can't open $project: $!\n";
my %input;
while(my $line = <FILE>) {
  chomp $line; # Get rid of whitespace (newline) at the end of the string
  if($line =~ /\tCM+(\d*)/io) {
    $input{$1}++;
  }
}
close(FILE);

##</code><code>##

open(OUT, '>>', 'project.out') or die "Can't open project.out for writing: $!\n";
foreach my $i (keys %input) {
  print OUT "$i\n" unless $input{$i} > 1;
}
close OUT;