<p>The server cannot read or write a mysql.* native table because its actual column layout differs from the definition expected by the running MySQL binaries.</p>
<p>MySQL Error 1682: ER_WRONG_NATIVE_TABLE_STRUCTURE signals that a system table in the mysql schema is out of sync with the current server version. Run mysql_upgrade or rebuild the affected table to align its structure and restart the server.</p>
Native table '%s'.'%s' has the wrong structure
MySQL raises error 1682 with the message Native table '%s'.'%s' has the wrong structure when it detects a mismatch between the on-disk definition of a mysql.* native table and the definition compiled into the server binary.
The server halts or rejects queries because inconsistent native tables risk corrupting metadata, privileges, and performance statistics. Fixing the mismatch quickly restores normal startup and statement execution.
A version upgrade that skipped mysql_upgrade is the most common trigger. The data dictionary schema changed, but the tables on disk remain on the old layout, triggering a structure check failure.
Manual ALTER TABLE or DROP COLUMN commands issued against mysql.* tables also lead to column count or type differences that the server flags as unsafe.
Running an older mysqld binary on a newer datadir (or vice versa) introduces incompatible structures that the server immediately rejects.
First, stop the MySQL service to prevent further access. Back up the entire data directory before making changes.
Next, run mysql_upgrade with the same major version as the running server. This utility automatically recreates or alters system tables to the expected definitions.
If mysql_upgrade is unavailable, manually recreate the offending table: dump its data, drop it, run the CREATE TABLE statement from the MySQL source scripts, and reload the data.
After a minor upgrade from 5.7 to 8.0 on Ubuntu, the server fails to start with error 1682. Running sudo mysql_upgrade -u root -p followed by systemctl restart mysql resolves the issue.
On a development laptop, a developer accidentally altered mysql.user. Restoring the table from a fresh installation dump and flushing privileges clears the mismatch.
Always execute mysql_upgrade or the in-place upgrade command whenever you change MySQL versions, even for minor releases.
Avoid direct DDL on mysql.* tables. Use dedicated statements such as CREATE USER, GRANT, or FLUSH instead. Enforce this policy through role privileges.
Galaxy users can embed upgrade checks inside automated workflows, ensuring every CI pipeline verifies system table consistency after deployment.
ER_TABLE_DEF_CHANGED occurs when a regular user table definition differs from its metadata cache. A DROP and CREATE or an ALTER TABLE ... FORCE usually fixes it.
ER_INCORRECT_GLOBAL_LOCAL_VAR signals a conflict in global variables after upgrade and is often resolved by running mysql_upgrade alongside error 1682.
The binaries were updated, but mysql_upgrade was not executed, leaving system tables on the old schema.
A direct ALTER TABLE, DROP COLUMN, or CHANGE COLUMN against tables like mysql.user modified the expected layout.
The datadir belongs to a newer version but the server binary is older (or vice versa), causing schema incompatibility.
File system issues or abrupt power loss damaged frm or ibd files, making column definitions unreadable by the server.
Regular table definition mismatch; often fixed with ALTER TABLE ... FORCE.
Variable mismatch after upgrade; resolved by mysql_upgrade.
Unknown column type in frm; indicates corruption or version conflict.
No. Ignoring the mismatch risks metadata corruption and prevents normal server operation.
Yes. The server must be started and often restarted, so plan a maintenance window.
Dumping mysql.* tables, recreating them, and reloading data aligns structures but is more manual than mysql_upgrade.
Galaxy can integrate upgrade scripts into CI, flagging any schema mismatch before production deployment.
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