I logged into my mysql server and figured out mysql used almost 70% of allocated space. So… time to clean flush and reset binary logs (I don’t use expire_logs_days).
$> mysql -u root -p mysql> FLUSH LOGS; mysql> RESET MASTER;
That’s it. After that the usage reduced to 5% of allocated space.
Another option is to use expire_logs_days option in my.cnf file.