Hello Azaghal,

The bottleneck occurs here, in the inner loop:

while (my $line = <$fh>) {
    chomp $line;
    foreach my $mot (keys (%count)) {
    chomp $mot;        
    foreach my $str ($line =~ /$mot/g) {
        $count{$str}++;
    }
    }    
}
[download]

If %count contains 60,000 entries, then the foreach loop performs 60,000 regex tests against each line of the input text file! Fortunately, this is quite unnecessary. I would split each line into words and simply lookup these words in the hash; like this (untested):

while (my $line = <$fh>)
{
    chomp $line;

    my @words = split /\W+/, $line;

    for my $word (@words)
    {
        ++$count{$word} if exists $count{$word};
    }
}
[download]

(You may need to tweak the split regex, depending on the contents of the words in the list file.)

Hope that helps,