Addressing MySQL Error 1039 (ER_UNEXPECTED_EOF): Strategies for Resolving Unexpected EOF Issues

When you encounter Error 1039 in MySQL, with the SQLSTATE code HY000, it signifies that an “Unexpected EOF (End of File)” was encountered when reading a file. This error often points to issues with file corruption or truncation that MySQL did not expect when attempting to read a database file.

Understanding Error 1039 – SQLSTATE: HY000 (ER_UNEXPECTED_EOF)

The Error 1039 message “Unexpected EOF found when reading file ‘%s’ (errno: %d)” indicates that MySQL attempted to read more data from a file than was available. This can happen for various reasons, such as file corruption, disk issues, or incomplete writes. The ‘%s’ in the message will be replaced by the filename, and ‘%d’ will be replaced by the system error number, providing more context for troubleshooting.

Diagnosing the Issue

To diagnose Error 1039, follow these steps:

  1. Note the filename and error number given in the error message.
  2. Check the MySQL error log for additional context surrounding the error.
  3. Inspect the mentioned file’s size and compare it with what MySQL expects.
  4. Verify the disk’s integrity and check for any signs of hardware failure.

Fixing the Error

Example 1: Repairing MyISAM Tables

For MyISAM tables, you can use the myisamchk tool to repair the table files:

myisamchk --recover /path/to/mysql/data/dir/tablename.MYI

Replace /path/to/mysql/data/dir/ with the actual path to your MySQL data directory and tablename with the name of the affected table.

Example 2: Restoring from Backup

If a table is too corrupted to be repaired, restoring from a backup is the safest approach:

mysql -u username -p database_name < backup_file.sql

Replace username, database_name, and backup_file.sql with your actual MySQL username, database name, and backup file.

Example 3: Checking Disk Space

A full disk can cause incomplete file writes. Check your disk space with:

df -h

If the disk is full, free up space by removing unnecessary files or expanding the disk.

Example 4: Filesystem Check

Run a filesystem check to look for and repair any filesystem corruption that might cause file truncation:

fsck /dev/sdX

Replace /dev/sdX with the device identifier for your disk.

Example 5: Increasing Open Files Limit

If the system’s open files limit is too low, it can lead to file handling errors. Check and increase the limit if necessary:

ulimit -n
ulimit -n 4096

The first command checks the current limit, and the second command sets a new limit.

Example 6: Checking for External File Modifications

Ensure that no external processes are incorrectly modifying or truncating MySQL files. Use tools like lsof to check which processes are accessing your MySQL files:

lsof /path/to/affected/file

Example 7: Rebuilding Tables

For InnoDB tables, use the ALTER TABLE command to rebuild the table and potentially fix the EOF error:


Replace tablename with the name of your table.


MySQL Error 1039 is typically related to file corruption or system-level issues. By carefully following the steps and examples provided, you can identify the root cause and apply the appropriate solution to resolve the error. Regular database backups and file system checks can help mitigate the risk of such errors and ensure the stability of your MySQL databases.

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