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use warnings;
use strict;
...
    print "Site $site: ", join(", ",
        sort {$a<=>$b} keys %{ $sites{$site} } ), "\n";
}

my %alldsks = map {$_=>1} keys %dsks;
for my $site (sort {$a<=>$b} keys %sites) {
...
Site 512 MISSING: 71, 96, 97, 204, 205, 206, 207, 550, 551, 554
Site 587 MISSING: 70, 71, 90, 91, 92, 93, 96, 97, 189, 190, 204, 205, 
+206, 207
Site 1108 MISSING: 90, 91, 92, 93, 96, 97, 189, 190, 550, 551, 554