Query log was turned on actually, but we couldn't find the problem so easily.. at the end, we found out that there are few wordpress queries that slow down the site, and many other users experienced same problems..
Queries were like this:
SELECT SQL_CALC_FOUND_ROWS wp_posts.* FROM wp_posts WHERE 1=1 AND ( wp_posts.ID IN (
SELECT object_id
FROM wp_term_relationships
WHERE term_taxonomy_id IN (1,461)
GROUP BY object_id HAVING COUNT(object_id) = 2
) ) AND wp_posts.post_type = 'post' AND (wp_posts.post_status = 'publish') GROUP BY wp_posts.ID ORDER BY wp_posts.post_date DESC LIMIT 0, 6;
I've been told that queries like this go into all rows in the wp_posts and wp_comments tables, and we had there at least 80.000 rows. When we shut down MySQL, MySQL log returned something like this - Sorting aborted, and at least 10 threads like this..
After we deleted nearly 40.000 comments from our database, site started to work normally.. well, in the past 36 hours it's working fine, and it's a new record i would say, after two weeks of problems..