To enable slow query log in cpanel server, you can use following steps.
Add following to following to /etc/my.cnf file on server.
# vi /etc/my.cnf
After that, do the following commands to create the file with the right ownership and file permissions
# touch /var/lib/mysql/slow.log
# chmod 660 /var/lib/mysql/slow.log
# chown mysql:mysql /var/lib/mysql/slow.log
Restart the mysql server and check the logs in /var/lib/mysql/slow.log.