# Percona xtrabackup restore \[ERROR\] --initialize specified but the data directory has files in it. Aborting

**URL:** <https://forums.percona.com/t/percona-xtrabackup-restore-error-initialize-specified-but-the-data-directory-has-files-in-it-aborting/24255>\
**Category:** Percona XtraBackup\
**Created:** [August 7, 2023, 8:18am UTC](https://forums.percona.com/t/percona-xtrabackup-restore-error-initialize-specified-but-the-data-directory-has-files-in-it-aborting/24255 "2023-08-07T08:18:33Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![seqwait](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/seqwait/32/12115_2.png) [@seqwait](https://forums.percona.com/u/seqwait)\
**Post date:** [August 7, 2023, 8:18am UTC](https://forums.percona.com/t/percona-xtrabackup-restore-error-initialize-specified-but-the-data-directory-has-files-in-it-aborting/24255/1 "2023-08-07T08:18:33Z")

</div>

xtrabackup version: 2.4  
mysql version: docker mysql5.7  
**step 1: backup**

```auto
innobackupex --defaults-file=~/.my.cnf.bak --user=root --password="123456" --databases=kk --backup /data/backups/

```

**step 2: start a new mysql**

```auto
docker run -d --name=mysqltt -p 3307:3306 \
    -e TZ=Asia/Shanghai \
    -e MYSQL_ROOT_PASSWORD=123456 \
    -v /alidata1/mysql_multi/data3307/mydata:/var/lib/mysql \
    mysql:5.7 --character-set-server=utf8mb4 \
    --collation-server=utf8mb4_unicode_ci

```

**step 3: apply-log**

```auto
innobackupex --apply-log --redo-only /data/backups/2023-08-07_15-29-16/

```

**step 4: restore**

```auto
docker stop mysqltt

rm -rf /alidata1/mysql_multi/data3307/mydata/*

innobackupex --copy-back --datadir=/alidata1/mysql_multi/data3307/mydata/ /data/backups/2023-08-07_15-29-16/

```

step: start mysqltt

```auto
docker start mysqltt 

```

**the error**

```auto
2023-08-07 16:04:18+08:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.36-1debian10 started.
2023-08-07 16:04:19+08:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
2023-08-07 16:04:19+08:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.36-1debian10 started.
2023-08-07 16:04:19+08:00 [Note] [Entrypoint]: Initializing database files
2023-08-07T08:04:19.211882Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2023-08-07T08:04:19.213398Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2023-08-07T08:04:19.213431Z 0 [ERROR] Aborting

```

---

<div class="post-metadata">

**Author:** ![Denis\_Subbota](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/denis_subbota/32/23607_2.png) [@Denis\_Subbota](https://forums.percona.com/u/Denis_Subbota)\
**Post date:** [August 7, 2023, 9:39am UTC](https://forums.percona.com/t/percona-xtrabackup-restore-error-initialize-specified-but-the-data-directory-has-files-in-it-aborting/24255/2 "2023-08-07T09:39:11Z")

</div>

Hello seqwait,  
As per the error log docker container is trying to start with a freshly created mysql directory and it’s trying to run mysqld --initialize

```auto
2023-08-07T08:04:19.213398Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.

```

In entrypoint scipt i found these functions:

> you may found script you have by  
> docker exec -ti mysqltt /bin/bash  
> and  
> cat entrypoint.sh

```auto

# initializes the database directory
docker_init_database_dir() {
	mysql_note "Initializing database files"
	"$@" --initialize-insecure --default-time-zone=SYSTEM
	mysql_note "Database files initialized"
}

```

and it should not be running if you have something in directory:

```auto
...
docker_setup_env() {
	# Get config
	declare -g DATADIR SOCKET
	DATADIR="$(mysql_get_config 'datadir' "$@")"
	SOCKET="$(mysql_get_config 'socket' "$@")"

	# Initialize values that might be stored in a file
	file_env 'MYSQL_ROOT_HOST' '%'
	file_env 'MYSQL_DATABASE'
	file_env 'MYSQL_USER'
	file_env 'MYSQL_PASSWORD'
	file_env 'MYSQL_ROOT_PASSWORD'

	declare -g DATABASE_ALREADY_EXISTS
	if [-d "$DATADIR/mysql"]; then
		DATABASE_ALREADY_EXISTS='true'
	fi
}
...
	if [-z "$DATABASE_ALREADY_EXISTS"]; then
			docker_verify_minimum_env

			# check dir permissions to reduce likelihood of half-initialized database
			ls /docker-entrypoint-initdb.d/ > /dev/null

			docker_init_database_dir "$@"

			mysql_note "Starting temporary server"
			docker_temp_server_start "$@"
			mysql_note "Temporary server started."

			mysql_socket_fix
			docker_setup_db
			docker_process_init_files /docker-entrypoint-initdb.d/*

			mysql_expire_root_user

			mysql_note "Stopping temporary server"
			docker_temp_server_stop
			mysql_note "Temporary server stopped"

			echo
			mysql_note "MySQL init process done. Ready for start up."
			echo
		else
			mysql_socket_fix
		fi
	fi
	exec "$@"

```

Could you please check if you have files in and also if mysql directory is there database

```auto
/alidata1/mysql_multi/data3307/mydata/

```

also you may inspect entrypoint.sh for more info

Regards,  
Denis Subbota.  
Managed Services, Percona.

---

<div class="post-metadata">

**Author:** ![matthewb](https://sea1.discourse-cdn.com/flex019/user_avatar/forums.percona.com/matthewb/32/34_2.png) [@matthewb](https://forums.percona.com/u/matthewb)\
**Post date:** [August 7, 2023, 3:27pm UTC](https://forums.percona.com/t/percona-xtrabackup-restore-error-initialize-specified-but-the-data-directory-has-files-in-it-aborting/24255/3 "2023-08-07T15:27:43Z")

</div>

Hello @seqwait,  
`innobackupex` is an extremely old and dead tool. What modern documentation did you read to use this tool instead of `xtrabackup`?