It trains only for mail in the myspam folder under john1. You need to get all the spam into that folder. When I did it, I told my users to add the spam mailbox to their own email client so they could move their spam into it.
There is a straightforward way to have spam automatically deleted. You accomplish this with an email filter (cPanel | Email | Filtering). Set up a filter that says if the "Spam Assassin header" "begins with" "Yes" then "discard". Just be sure to set your spam score high enough so as not to automatically delete something good, and maintain a good whitelist for your friends or customers. Note that if you use this method to delete spam, it's not necessary to have SA set to "rewrite headers".
Our account gets about 2500 spams a day, so we find auto-delete a necessity.