Enable slow query log in MySQL

# touch /var/log/mysql/mysql-slow.log

# chown mysql:mysql /var/log/mysql/mysql-slow.log

If you want to leave slow query logging on, you will need to add 3 lines to /etc/mysql/my.cnf under the [mysqld] section:

slow_query_log=1
slow_query_log_file=/var/log/mysql/mysql-slow.log
long_query_time=2

Restart your mysql :- 

#/etc/init.d/mysqld restart

To test if it is working correctly, simply run a SELECT SLEEP(x) query where "x" is longer than the long_query_time

root@anneke:~# mysql -e 'SELECT SLEEP(5);'

Then you can look at the logfile and check id your "slow" query is there:

less /var/log/mysql/mysql-slow.log