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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 CGI programming In reply to Re^3: Problem in creating Directory
by lune
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