getting rid of duplicates too:
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
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