Thanks for the reply dave, yes ur ryt i havent done proper deligence, becoz am new to perl , and my perl knowledge is not upto the mark ,
when i changed accordingly its giving following error
Failed to createeate directory /var/www/html/piRNA_html/UNAFold/output//: File exists at /var/www/html/piRNA_html/UNAFold/mkdirtest.cgi line 39.