It is working now: this is my final code

#!/usr/bin/perl
use warnings;
use strict;

my %contig;
open (my $CNTG, '<', $ARGV[0]) or die $!;
while (<$CNTG>) {
    chomp;
#    s///;  # Remove the underscore, as it doesn't appear in the genba
+nk.
    $contig{$_} = 1;
#    print $_;
}

local $/ = '//';  # Read the file one record a time.
open (my $GB, '<', $ARGV[1]) or die $!;
while (<$GB>) {
    if (my ($id) = /LOCUS \s+ \S+ _ (contig [0-9]+)/x) {
        print if $contig{$id};
    }
}
~
[download]

THANKS!