I have just encountered this issue as well. After upgrading the server would not start with the same error message as the original server. I do use InnoDB databases by default.
Output of my syslog: Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 [Note] Plugin 'FEDERATED' is disabled. Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 InnoDB: The InnoDB memory heap is disabled Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 InnoDB: Mutexes and rw_locks use GCC atomic builtins Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 InnoDB: Compressed tables use zlib 1.2.7 Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 InnoDB: Using Linux native AIO Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 InnoDB: Initializing buffer pool, size = 16.0M Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 InnoDB: Completed initialization of buffer pool Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 InnoDB: highest supported file format is Barracuda. Dec 18 17:42:04 localhost mysqld_safe[30287]: 131218 17:42:04 InnoDB: Waiting for the background threads to start Dec 18 17:42:05 localhost mysqld_safe[30287]: 131218 17:42:05 InnoDB: 5.5.33 started; log sequence number 1595675 Dec 18 17:42:05 localhost mysqld_safe[30287]: 131218 17:42:05 InnoDB: !!! innodb_force_recovery is set to 1 !!! Dec 18 17:42:05 localhost mysqld_safe[30287]: #007/usr/sbin/mysqld: File './mysql-bin.000116' not found (Errcode: 13) Dec 18 17:42:05 localhost mysqld_safe[30287]: 131218 17:42:05 [ERROR] Failed to open log (file './mysql-bin.000116', errno 13) Dec 18 17:42:05 localhost mysqld_safe[30287]: 131218 17:42:05 [ERROR] Could not open log file Dec 18 17:42:05 localhost mysqld_safe[30287]: 131218 17:42:05 [ERROR] Can't init tc log Dec 18 17:42:05 localhost mysqld_safe[30287]: 131218 17:42:05 [ERROR] Aborting Dec 18 17:42:05 localhost mysqld_safe[30287]: Dec 18 17:42:05 localhost mysqld_safe[30287]: 131218 17:42:05 InnoDB: Starting shutdown... Dec 18 17:42:06 localhost mysqld_safe[30287]: 131218 17:42:06 InnoDB: Shutdown completed; log sequence number 1595675 Dec 18 17:42:06 localhost mysqld_safe[30287]: 131218 17:42:06 [Note] /usr/sbin/mysqld: Shutdown complete Dec 18 17:42:06 localhost mysqld_safe[30287]: I noticed the server was having issues finding mysql-bin.000116 although that file did exist in the data directory. Having found it I discovered the permissions for that file where set to root while the other files where set to mysql. -rw-rw---- 1 mysql root 25977 Dec 18 17:33 mysql-bin.000113 -rw-rw---- 1 mysql root 1061358 Dec 18 17:33 mysql-bin.000114 -rw-rw---- 1 root root 25977 Dec 18 17:41 mysql-bin.000115 -rw-rw---- 1 root root 1061358 Dec 18 17:41 mysql-bin.000116 <---- Changing the permissions on these two files to mysql enabled the server to start. That said doing apt-get upgrade afterwards to complete the upgrade and once creates another mysql-bin file with the wrong permissions and bails out reproducing the problem. While I can't complete the configure stage I can now at least get the server running again. I hope this helps you to track down this bug.