... I initialized my hashes and the  $s1{animal_id} = 0; part too.

In addition to the other replies, and in case you have not already realized it, the statements
    $s1{animal_id} = 0;
    $s2{animal_id} = 0;
do nothing in the context of the code you have shown. What they actually do is to set the value of the key  'animal_id' to 0 in both the  %s1 and  %s2 hashes on each pass through the  while loop. No further reference is made to this key in these hashes in the code shown. The keys contained in the scalar variable  $animal_id seem to have a format like  'a19' (as far as I can tell from the confusingly formatted OP), and are nothing like  'animal_id'.

The other point to understand is that creating an empty hash (as all hashes and arrays are when created) and then initializing it as an empty hash is not really 'initializing' it in any programatic sense. The only purpose, IMO, of a statement like
    my %s1 = ();
is to say 'yes, I really do mean this hash to be empty at this point', thus obviating the need to type out an explicit comment to this effect – which may be a very useful side effect!