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If you are running an HA setup where there are multiple mysql servers, then you can see the error

2006, 'MySQL server has gone away

as it refers to the fact that the connection has been closed for some reason. This can be for a variety of reasons including haproxy moving the connection to another endpoint, or that the connection idle long enough that the socket was closed.

https://dev.mysql.com/doc/refman/5.0/en/gone-away.html