You've reported at least two completely different errors in this thread, "file exists", and "permission denied". For "permission denied", do this:
ls -ld /var/www/html/piRNA_html/UNAFold/output

[download]

What are the permissions on the directory? Do you (or the user this script is running under) have write permission in the directory?

In reply to Re^3: Problem in creating Directory by runrig
in thread problem in mkdir by MVRS

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