You can not run the jobqueue manualy from the interface, as the interface does not have permissions for that and it can not have permissions for that as the jobqueue can only be executed by the root user.
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How can I make a PHP file run the script as root and not apache.
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You cant without opening up your system for hackers. The apache webserver may naver be run as root user, thats even compiled into the apache binaries of all linux distributions to prevent such a configuration.