Magento – Magento cron job disappearing

You should not call/run cron.php directly but cron.sh via system cronjob/crontab instead.

I can recommend Fabrizios Blogpost for more information about the Magento cron:

cron.php vs. cron.sh

In Magento’s root folder there’s a cron.php file and a cron.sh file. Briefly explained cron.sh internally calls cron.php and takes care of not executing more than one process in parallel. That’s a good thing, right? Well, sometimes… If you have long running tasks (e.g. a product import implemented as a task), these tasks will prevent anything else from being executed until the task has finished. You might have some other important tasks that shouldn’t wait or be skipped just because another task is running. Check the “Missed if Not Run Within” setting to configure the maximum delay a task can have to still be executed.

On the other hand using cron.php will start a new process every time it’s being called which could easily result in performance problems or race conditions for tasks operating on the same data. This is why cron.php should not be called directly. Find out more about cron groups later in this blog post for a nice solution on how to handle this situation.

http://www.webguys.de/magento/tuerchen-08-magento-cron-demystified/

Please Try This

It looks like you're using the default Magento cron.

If you want the AOE Scheduler to work you need to use the scheduler's cron instead - e.g.:

*/5 * * * * /bin/sh -f /home/cpanel_user/public_html/scheduler_cron.sh

FYI - the "heartbeat" task is a very lightweight cron job that runs every time, simply reporting that the scheduler is running. If your message is showing you that the heartbeat couldn't be found it likely means either that your cron isn't configured correctly, or there's a lock in place. You can try removing var/locks and the scheduler's lock which normally lives in /tmp if this is the case.

Hope It's helpful for any one.