After June 1st 2015 we'll be enforcing strict limits on MySQL queries. All queries longer than 30 minutes (1800 seconds) will be terminated and the transformation will fail. You can now see duration of all queries longer than 2 minutes (120 seconds) in event log of any Transformation job so you can take optimization steps in advance.
We're introducing this limit to prevent errors like forgotten indexes and also to balance load on the shared MySQL Transformation database.
If your queries take significantly longer time than 30 minutes, please consider migrating your project to Redshift.