The --upgrade-system-tables option was used, user tables won't be touched. Phase 1/7: Checking and upgrading mysql database Processing databases mysql mysql.column_stats OK mysql.columns_priv OK mysql.db OK mysql.event OK mysql.func OK mysql.gtid_slave_pos OK mysql.help_category OK mysql.help_keyword OK mysql.help_relation OK mysql.help_topic OK mysql.host OK mysql.index_stats OK mysql.innodb_index_stats Error : Unknown storage engine 'InnoDB' error : Corrupt mysql.innodb_table_stats Error : Unknown storage engine 'InnoDB' error : Corrupt mysql.plugin OK mysql.proc OK mysql.procs_priv OK mysql.proxies_priv OK mysql.roles_mapping OK mysql.servers OK mysql.table_stats OK mysql.tables_priv OK mysql.time_zone OK mysql.time_zone_leap_second OK mysql.time_zone_name OK mysql.time_zone_transition OK mysql.time_zone_transition_type OK mysql.transaction_registry Error : Unknown storage engine 'InnoDB' error : Corrupt mysql.user OK Repairing tables mysql.innodb_index_stats Error : Unknown storage engine 'InnoDB' error : Corrupt mysql.innodb_table_stats Error : Unknown storage engine 'InnoDB' error : Corrupt mysql.transaction_registry Error : Unknown storage engine 'InnoDB' error : Corrupt Phase 2/7: Installing used storage engines... Skipped Phase 3/7: Fixing views... Skipped Phase 4/7: Running 'mysql_fix_privilege_tables' Phase 5/7: Fixing table and database names ... Skipped Phase 6/7: Checking and upgrading tables... Skipped Phase 7/7: Running 'FLUSH PRIVILEGES' OK