When you create a file or directory, you can define the permissions for the item you are going to create. These are the 0777 permissions given by You.
As creating a new directory is nothing else but writing an entry into the directory above, you need write permissions for /var/www/html/piRNA_html/UNAFold/output.
The user that needs those permissions is the cgi user, the script will run under.
Here You can find some hints on
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Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
<code> <a> <b> <big>
<blockquote> <br /> <dd>
<dl> <dt> <em> <font>
<h1> <h2> <h3> <h4>
<h5> <h6> <hr /> <i>
<li> <nbsp> <ol> <p>
<small> <strike> <strong>
<sub> <sup> <table>
<td> <th> <tr> <tt>
Snippets of code should be wrapped in
<code> tags not
<pre> tags. In fact, <pre>
tags should generally be avoided. If they must
be used, extreme care should be
taken to ensure that their contents do not
have long lines (<70 chars), in order to prevent
horizontal scrolling (and possible janitor
Want more info? How to link or
or How to display code and escape characters
are good places to start.