Plesk Update fails: Table 'mysql.innodb_index_stats' doesn't exist in engine

Kuzma Ivanov

Updated August 06, 2025 03:09

Plesk for Linux kb: technical

Applicable to:

Plesk for Linux
Plesk for Windows

Symptoms

Plesk update fails due to corrupted InnoDB table(s): mysql.innodb_index_stats, mysql.innodb_table_stats, mysql.transaction_registry, mysql.gtid_slave_pos:

CONFIG_TEXT: Error : Table 'mysql.innodb_index_stats' doesn't exist in engine
...
Error : Table 'mysql.innodb_table_stats' doesn't exist in engine
...
Error : Table 'mysql.transaction_registry' doesn't exist in engine
...
Error : Table 'mysql.gtid_slave_pos' doesn't exist in engine
One of the errors above also appears when creating a database dump of the mysql database, installing SpamAssassin Spam Filter or running plesk repair db.

Cause

Corrupted InnoDB tables in the mysql database.

Resolution

For Plesk on Linux

Connect to the Plesk server via SSH.
Create a temporary backup directory:

# mkdir -p /root/backup_folder/
Stop the MySQL/MariaDB service:

# service mariadb stop
Move the .frm and .ibd files of the corrupted table(s) that was mentioned in the error message:

# mv /var/lib/mysql/mysql/innodb_index_stats* /root/backup_folder/

# mv /var/lib/mysql/mysql/innodb_table_stats* /root/backup_folder/

# mv /var/lib/mysql/mysql/transaction_registry* /root/backup_folder/

# mv /var/lib/mysql/mysql/gtid_slave_pos.* /root/backup_folder/
Start the MySQL/MariaDB service:

# service mariadb start
Access the Plesk database:

# plesk db
Switch to the MySQL/MariaDB database:

MYSQL_LIN: MariaDB [psa]> use mysql;
Remove the table(s) from the mysql database (if exists):

MYSQL_LIN: MariaDB [mysql]> drop table innodb_index_stats;

MYSQL_LIN: MariaDB [mysql]> drop table innodb_table_stats;

MYSQL_LIN: MariaDB [mysql]> drop table transaction_registry;

MYSQL_LIN: MariaDB [mysql]> drop table gtid_slave_pos;
Recreate the table:
- innodb_index_stats
  
  MYSQL_LIN: MariaDB [mysql]> CREATE TABLE `innodb_index_stats` (
  `database_name` varchar(64) NOT NULL,
  `table_name` varchar(199) NOT NULL,
  `index_name` varchar(64) NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT current_timestamp() ON UPDATE current_timestamp(),
  `stat_name` varchar(64) NOT NULL,
  `stat_value` bigint(20) unsigned NOT NULL,
  `sample_size` bigint(20) unsigned DEFAULT NULL,
  `stat_description` varchar(1024) NOT NULL,
  PRIMARY KEY (`database_name`,`table_name`,`index_name`,`stat_name`)
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0;
- innodb_table_stats
  
  MYSQL_LIN: MariaDB [mysql]> CREATE TABLE `innodb_table_stats` (
  `database_name` varchar(64) NOT NULL,
  `table_name` varchar(199) NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT current_timestamp() ON UPDATE current_timestamp(),
  `n_rows` bigint(20) unsigned NOT NULL,
  `clustered_index_size` bigint(20) unsigned NOT NULL,
  `sum_of_other_index_sizes` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`database_name`,`table_name`)
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0;
- transaction_registry
  
  MYSQL_LIN: MariaDB [mysql]> CREATE TABLE `transaction_registry` (
  `transaction_id` bigint(20) unsigned NOT NULL,
  `commit_id` bigint(20) unsigned NOT NULL,
  `begin_timestamp` timestamp(6) NOT NULL DEFAULT '0000-00-00 00:00:00.000000',
  `commit_timestamp` timestamp(6) NOT NULL DEFAULT '0000-00-00 00:00:00.000000',
  `isolation_level` enum('READ-UNCOMMITTED','READ-COMMITTED','REPEATABLE-READ','SERIALIZABLE') NOT NULL,
  PRIMARY KEY (`transaction_id`),
  UNIQUE KEY `commit_id` (`commit_id`),
  KEY `begin_timestamp` (`begin_timestamp`),
  KEY `commit_timestamp` (`commit_timestamp`,`transaction_id`)
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0;
- gtid_slave_pos
  
  MYSQL_LIN: CREATE TABLE `gtid_slave_pos` (
  `domain_id` int(10) unsigned NOT NULL,
  `sub_id` bigint(20) unsigned NOT NULL,
  `server_id` int(10) unsigned NOT NULL,
  `seq_no` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`domain_id`,`sub_id`))
  ENGINE=MyISAM DEFAULT CHARSET=utf8 COMMENT='Replication slave GTID state';
Exit MySQL/MariaDB:

MYSQL_LIN: MariaDB [mysql]> exit
Restart the MySQL/MariaDB service:

# service mariadb restart
Update Plesk.
Remove the temporary backup directory:

# rm -f /root/backup_folder/

For Plesk on Windows Server

Connect to the Plesk server via RDP.
Start a command prompt as an Administrator.
Stop PleskSQLServer service:

C:\> net stop PleskSQLServer
Open %plesk_dir%MySQL\Data\mysql in Windows Explorer.
Remove the .frm and .ibd files of the corrupted table(s) that was mentioned in the error message.
Start PleskSQLServer service:

C:\> net start PleskSQLServer
Access the Plesk database:

C:\> plesk db
Switch to the MySQL/MariaDB database:

MYSQL_WIN: MariaDB [psa]> use mysql;
Remove the table(s) from the mysql database (if exists):

MYSQL_WIN: MariaDB [mysql]> drop table innodb_index_stats;

MYSQL_WIN: MariaDB [mysql]> drop table innodb_table_stats;

MYSQL_WIN: MariaDB [mysql]> drop table transaction_registry;

MYSQL_WIN: MariaDB [mysql]> drop table gtid_slave_pos;
Recreate the table(s):
- innodb_index_stats
  
  MYSQL_WIN: CREATE TABLE `innodb_index_stats` (
  `database_name` varchar(64) NOT NULL,
  `table_name` varchar(199) NOT NULL,
  `index_name` varchar(64) NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT current_timestamp() ON UPDATE current_timestamp(),
  `stat_name` varchar(64) NOT NULL,
  `stat_value` bigint(20) unsigned NOT NULL,
  `sample_size` bigint(20) unsigned DEFAULT NULL,
  `stat_description` varchar(1024) NOT NULL,
  PRIMARY KEY (`database_name`,`table_name`,`index_name`,`stat_name`)
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0;
- innodb_table_stats
  
  MYSQL_WIN: CREATE TABLE `innodb_table_stats` (
  `database_name` varchar(64) NOT NULL,
  `table_name` varchar(199) NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT current_timestamp() ON UPDATE current_timestamp(),
  `n_rows` bigint(20) unsigned NOT NULL,
  `clustered_index_size` bigint(20) unsigned NOT NULL,
  `sum_of_other_index_sizes` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`database_name`,`table_name`)
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0;
- transaction_registry
  
  MYSQL_WIN: CREATE TABLE `transaction_registry` (
  `transaction_id` bigint(20) unsigned NOT NULL,
  `commit_id` bigint(20) unsigned NOT NULL,
  `begin_timestamp` timestamp(6) NOT NULL DEFAULT '0000-00-00 00:00:00.000000',
  `commit_timestamp` timestamp(6) NOT NULL DEFAULT '0000-00-00 00:00:00.000000',
  `isolation_level` enum('READ-UNCOMMITTED','READ-COMMITTED','REPEATABLE-READ','SERIALIZABLE') NOT NULL,
  PRIMARY KEY (`transaction_id`),
  UNIQUE KEY `commit_id` (`commit_id`),
  KEY `begin_timestamp` (`begin_timestamp`),
  KEY `commit_timestamp` (`commit_timestamp`,`transaction_id`)
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0;
- gtid_slave_pos
  
  MYSQL_WIN: CREATE TABLE `gtid_slave_pos` (
  `domain_id` int(10) unsigned NOT NULL,
  `sub_id` bigint(20) unsigned NOT NULL,
  `server_id` int(10) unsigned NOT NULL,
  `seq_no` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`domain_id`,`sub_id`))
  ENGINE=MyISAM DEFAULT CHARSET=utf8 COMMENT='Replication slave GTID state';
Exit MySQL/MariaDB:

MYSQL_WIN: MariaDB [mysql]> exit
Restart the MySQL/MariaDB service:

C:\> net stop PleskSQLServer

C:\> net start PleskSQLServer
Update Plesk.