My server's /var/ partition is filling up and I would like to know how to reduce the size of the quarantine directories and mailscanner mysql database.

Quarantined messages (which in the default installation are only messages with a potentially dangerous file attachment) are kept in the quarantine directory (/var/spool/MailScanner/quarantine) for seven days. To change the length of time quarantined message are saved, go to WHM > Plugins > ConfigServer MailScanner FE > MailControl, click the Menu button (top right), select MailControl Settings, and change the value for Keep x days of Quarantine entries.

The mailscanner MySQL database is also stored in the /var/ directory (/var/lib/mysql/mailscanner). The size of the MailScanner/MailWatch database is configured in the WHM front-end: WHM > Plugins > ConfigServer MailScanner FE > MailControl, > Menu button (top right) > MailControl Settings > "Keep x days of MySQL database entries". It's set to 30 by default but you can reduce this to whatever you want. A script will run daily to delete any entries older than the number of days this is set to.

If you want to empty out the entire database and start over, the easiest way is to delete the entire database using the shell command:

mysql -e "drop database mailscanner"

and then run the script:

/usr/mscpanel/mailcontrol/dbadd.pl

to recreate the database.