Getting times out despite server settings

SQL Error (2013): Lost connection to MySQL server during query

I keep getting this error after 5 mins when running long select statements despite the fact that my wait_timeout is 28800 and my interactive_timeout is 28800.

Any suggestions?

Check and see if this information will help you:

http://dev.mysql.com/doc/refman/5.5/en/gone-away.html
http://dev.mysql.com/doc/refman/5.5/en/mysql-select-db.html

Please also specify what exactly you are doing

I'm running a select statement on the server that takes longer than 5 minutes to run. Heidi gets disconnected after 5 mins despite wait_timeout is 28800 and interactive_timeout is 28800