Use of uninitialized value $count_in in printf at ../remove_duplicate
+_genes.pl line 34.

0 total records read from 'enzymes.fasta'

Use of uninitialized value $count_out in printf at ../remove_duplicate
+_genes.pl line 35.

0 records written to 'duplicate_gene_entries_in_enzymes.fasta' after r
+emoving duplicate entries
[download]

This is because you never increment the $count_in and $count_out variables in your code (and also did not provide a start value when you declared them).

BTW, there is a built-in variable, $., which keeps track of the number of lines read from a file. You can just print its value after you've finished reading your file (instead of $count_in).