On checking the disk usage of your server, you might notice that /root/.cpanel/comet consumes considerable amount of disk space.
This happens when high number of emails are in the mail queue manager which can occur when spamming is carried out in the server.
Manually purging the files would be an effort-consuming task.
Clear the comet directory by giving the following command via SSH:
# /usr/local/cpanel/bin/purge_dead_comet_files