Run a cron job on a controller method

What you should probably doing is not using the 'sessions' by default, instead you should have your 'web' controllers extending a MY_Controller which has the session/authentication code, and then the CLI controllers just extend the vanilla CI_Controller.

I use a lot of controllers run as CLI scripts, the syntax in my crontab looks like e.g:

/usr/bin/php /full/path/to/index.php controller method

The above all works for me in 2.X. I'm migrating my code to 3.X at the moment but haven't got to the CLIs so apologies if the above is not entirely true for 3.x.