/usr/local/cpanel/3rdparty/bin/sa-learn --no-sync --spam /home/username/mail/domain.com/account/.Junk/
To scan and add for ham (good email) run the following command:
/usr/local/cpanel/3rdparty/bin/sa-learn --no-sync -ham /home/username/mail/domain.com/account/Inbox/cur