Enable slow query log in MySQL
Turn on the Slow Query log in MySQL allow you to debug the sources of slow and problematic SQL.
To activate it, edit the MySQL configurations, e.g. /etc/my.cnf
[mysqld] ... ... log-slow-queries = /var/log/mysqld-slow.log long_query_time = 5
Restart MySQL and you will notice the file mysqld-slow.log will be created.
Any queries take more than 5 seconds to execute will be logged in this file.