What does it say if you print error message of mkdir? 
mkdir ("/var/www/html/piRNA_html/UNAFold/output/$temp2/$temp1",0775) o
+r print "in mkdir:$!";

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And maybe, you had better put your question not in "PerlMonks Discussion" but "Questions"...

In reply to Re: problem in mkdir by remiah
in thread problem in mkdir by MVRS

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