From the MySQL reference manual: For InnoDB tables, OPTIMIZE TABLE is mapped to ALTER TABLE, which rebuilds the table to update index statistics and free unused space in the clustered index.

Obviously the table is locked whilst it is being ALTER'd, rebuilding table index also takes some time.

I just ran the analyze script on the DB server and it took 28 minutes - do we still want this to be scheduled, if so on what frequency?
I think daily is too frequent, perhaps monthly would be OK to start with?

In any case... perhaps we could do this:

1) Put moodle.org in maintenance mode* (with a nice message).
2) Run statistics
3) Put moodle.org back to normal operation

*maintenance mode is one feature within Moodle that shows one maintenance message to everybody until disabled.

About frequency... well, the often, the better (specially for InnoDB, afaik), but if weekly (sundays) is too much (causing moodle.org to be under maintenance 1/2 hour weekly), then I think we could survive with a monthly approach.

Also, perhaps... it could have sense to run statistics for some tables often, leaving some heavy tables that don't get real benefit (like logs, caches...) to be calculated less frequently.

FYC, ciao