in reply to Fetch Mysql huge database

getting rid of duplicates too:
select username from table where username != '' and username not like 'deleted%' and username not in (select username from other_table) group by username having count(*) > 1;
I've never used mysql, but in other RDBMS systems I would check that enough memory has been assigned to buffer cache, sort area, hash sort area, etc. And by "enough", I mean "lots".

Joining two 34M rows on a decent enough server shouldn't take long. Nested iterations over 2 large tables does take a long time.

Having indexes on username on both tables would help a lot too