Найти таблица использующие myISAM:
SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;') FROM information_schema.tables WHERE engine='MyISAM' AND table_schema NOT IN ('information_schema','mysql','performance_schema');
В результате отобразится готовый набор команд:
+----------------------------------------------------------------------+
| CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;') |
+----------------------------------------------------------------------+
| ALTER TABLE dbname.wplg_comments ENGINE=InnoDB; |
| ALTER TABLE dbname.wplg_comments_blacklist ENGINE=InnoDB; |
| ALTER TABLE dbname.wplg_comments_objects ENGINE=InnoDB; |
| ALTER TABLE dbname.wplg_comments_reports ENGINE=InnoDB; |
| ALTER TABLE dbname.wplg_comments_settings ENGINE=InnoDB; |
| ALTER TABLE dbname.wplg_comments_subscriptions ENGINE=InnoDB; |
| ALTER TABLE dbname.wplg_comments_votes ENGINE=InnoDB; |
| ALTER TABLE dbname.tmp_upgrade_log ENGINE=InnoDB; |
| ALTER TABLE dbname.tmp_upgrade_tables ENGINE=InnoDB; |
+----------------------------------------------------------------------+
Исполняем каждую по очереди:
ALTER TABLE dbname.wplg_comments ENGINE=InnoDB;