In line 32, 58, and 59, you're calling mkdir, but not checking the "return value" (which is to say, not checking for success or failure). It's very important to check for failure, and if failure occurs, inspect the contents of the special variable "$!" to see what went wrong. Otherwise we're all just going to be guessing.

So, for example, on line 32, change to:

mkdir "/var/www/html/piRNA_html/UNAFold/output/$temp2/$temp1",
      0775
    or die "Failed to create directory ..../$temp2/$temp1: $!";
[download]

Once you know what went wrong 3/4ths of the battle is won. We could wade through the code, ask a bunch of questions, and so on. But unless you're taking advantage of Perl's ability to provide clues you haven't done your own due diligence yet. :)