Looks like logins to MySQL using both da_admin and da_roundcube are failing. If you haven't changed those MySQL passwords, then either someone or something else has, or MySQL is having some problems. Check the MySQL error log if there are any clues there. It should be in /usr/local/mysql/data/ with an .err extension. Rebuilding Roundcube will not resolve this, and I suspect it is not even relevant to the problem you're having, it's just a symptom.
No one had logged into any of the services. I have installed google authentication for SSH, Direct admin and many other services. My logs are also fine, no suspicious login attempts.
Note: I do had implemented this help after the issue (just for reference) (
https://help.directadmin.com/item.php?id=206)
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MySql Log
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15:58:26 mysqld_safe Starting mysqld daemon with databases from /var/li$
200805 15:58:27 [Note] /usr/sbin/mysqld (mysqld 5.5.60-MariaDB) starting as pr$
200805 15:58:28 InnoDB: The InnoDB memory heap is disabled
200805 15:58:28 InnoDB: Mutexes and rw_locks use GCC atomic builtins
200805 15:58:28 InnoDB: Compressed tables use zlib 1.2.7
200805 15:58:28 InnoDB: Using Linux native AIO
200805 15:58:28 InnoDB: Initializing buffer pool, size = 128.0M
200805 15:58:28 InnoDB: Completed initialization of buffer pool
200805 15:58:28 InnoDB: highest supported file format is Barracuda.
200805 15:58:29 InnoDB: Waiting for the background threads to start
200805 15:58:30 Percona XtraDB (
http://www.percona.com) 5.5.59-MariaDB-38.11 s$
200805 15:58:30 [Note] Plugin 'FEEDBACK' is disabled.
200805 15:58:30 [Note] Server socket created on IP: '0.0.0.0'.
200805 15:58:30 [Note] Event Scheduler: Loaded 0 events
200805 15:58:30 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.60-MariaDB' socket: '/var/lib/mysql/mysql.sock' port: 3306 Ma$
200806 20:03:18 [Note] /usr/sbin/mysqld: Normal shutdown
200806 20:03:18 [Note] Event Scheduler: Purging the queue. 0 events
200806 20:03:18 InnoDB: Starting shutdown...
200806 20:03:23 InnoDB: Shutdown completed; log sequence number 7548851
200806 20:03:23 [Note] /usr/sbin/mysqld: Shutdown complete
00806 22:03:23 mysqld_safe mysqld from pid file /var/lib/mysql/waseemabbas.pk$
200806 22:03:58 mysqld_safe Starting mysqld daemon with databases from /var/li$
200806 22:04:01 [Note] /usr/sbin/mysqld (mysqld 5.5.60-MariaDB) starting as pr$
200806 22:04:02 InnoDB: The InnoDB memory heap is disabled
200806 22:04:02 InnoDB: Mutexes and rw_locks use GCC atomic builtins
200806 22:04:02 InnoDB: Compressed tables use zlib 1.2.7
200806 22:04:02 InnoDB: Using Linux native AIO
200806 22:04:02 InnoDB: Initializing buffer pool, size = 128.0M
200806 22:04:02 InnoDB: Completed initialization of buffer pool
200806 22:04:02 InnoDB: highest supported file format is Barracuda.
200806 22:04:04 InnoDB: Waiting for the background threads to start
200806 22:04:05 Percona XtraDB (
http://www.percona.com) 5.5.59-MariaDB-38.11 s$
200806 22:04:05 [Note] Plugin 'FEEDBACK' is disabled.
200806 22:04:05 [Note] Server socket created on IP: '0.0.0.0'.
200806 22:04:05 [Note] Event Scheduler: Loaded 0 events
200806 22:04:05 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.60-MariaDB' socket: '/var/lib/mysql/mysql.sock' port: 3306 Ma$
200810 20:17:19 [Note] /usr/sbin/mysqld: Normal shutdown
'5.5.60-MariaDB' socket: '/var/lib/mysql/mysql.sock' port: 3306 Ma$
200810 20:17:19 [Note] /usr/sbin/mysqld: Normal shutdown
200810 20:17:19 [Note] Event Scheduler: Purging the queue. 0 events
200810 20:17:19 InnoDB: Starting shutdown...
200810 20:17:20 InnoDB: Waiting for 4 pages to be flushed
200810 20:17:21 InnoDB: Shutdown completed; log sequence number 106953355
200810 20:17:21 [Note] /usr/sbin/mysqld: Shutdown complete
200810 20:17:21 mysqld_safe mysqld from pid file /var/lib/mysql/waseemabbas.pk$
200810 20:19:27 mysqld_safe Starting mysqld daemon with databases from /var/li$
200810 20:19:30 [Note] /usr/sbin/mysqld (mysqld 5.5.60-MariaDB) starting as pr$
200810 20:19:31 InnoDB: The InnoDB memory heap is disabled
200810 20:19:31 InnoDB: Mutexes and rw_locks use GCC atomic builtins
200810 20:19:31 InnoDB: Compressed tables use zlib 1.2.7
200810 20:19:31 InnoDB: Using Linux native AIO
200810 20:19:32 InnoDB: Initializing buffer pool, size = 128.0M
200810 20:19:32 InnoDB: Completed initialization of buffer pool
200810 20:19:32 InnoDB: highest supported file format is Barracuda.
200810 20:19:33 InnoDB: Waiting for the background threads to start
200810 20:19:34 Percona XtraDB (
http://www.percona.com) 5.5.59-MariaDB-38.11 s$
200810 20:19:34 [Note] Plugin 'FEEDBACK' is disabled.