1) Timeout occurs when deleting repository. Check queries by using processlist. "show processlist;" 2) If the reason of that case is timeout, set follows. show variables like '%timeout'; set global innodb_lock_wait_timeout=300; set session innodb_lock_wait_timeout=300; If you necessary, kill process to restart process. "kill <id>;" 3) Check if you have dummy data. SELECT changesets.repository_id FROM changesets WHERE changesets.repository_id NOT IN (SELECT id from repositories) group by changesets.repository_id ; Do A or B. * A DELETE FROM changes WHERE changes.changeset_id IN (SELECT changesets.id FROM changesets WHERE changesets.repository_id NOT IN (SELECT id from repositories)); DELETE FROM changesets WHERE changesets.repository_id NOT IN (SELECT id from repositories); * or B (415 = your target repository id) DELETE FROM changes WHERE changes.changeset_id IN (SELECT changesets.id FROM changesets WHERE changesets.repository_id = 415);