I could not reproduce this with PS 5.6.21 and Xtrabackup 2.2.6. Can you able to provide exact steps for taking backup and apply-log? Taking backup for only "nil" DB. nilnandan@Dell-XPS:~$ sudo innobackupex --user=root --password=root --databases="nil" /home/nilnandan/backup [sudo] password for nilnandan: ... innobackupex: Using server version 5.6.21-70.1 innobackupex: Created backup directory /home/nilnandan/backup/2014-12-09_10-22-24 141209 10:22:24 innobackupex: Starting ibbackup with command: xtrabackup --defaults-group="mysqld" --backup --suspend-at-end --target-dir=/home/nilnandan/backup/2014-12-09_10-22-24 --innodb_log_file_size="50331648" --innodb_data_file_path="ibdata1:12M:autoextend" --tmpdir=/tmp --extra-lsndir='/tmp' --databases='nil' innobackupex: Waiting for ibbackup (pid=5653) to suspend innobackupex: Suspend file '/home/nilnandan/backup/2014-12-09_10-22-24/xtrabackup_suspended_2' xtrabackup version 2.2.6 based on MySQL server 5.6.21 Linux (x86_64) (revision id: ) xtrabackup: uses posix_fadvise(). xtrabackup: cd to /var/lib/mysql xtrabackup: open files limit requested 0, set to 1024 xtrabackup: using the following InnoDB configuration: xtrabackup: innodb_data_home_dir = ./ xtrabackup: innodb_data_file_path = ibdata1:12M:autoextend xtrabackup: innodb_log_group_home_dir = ./ xtrabackup: innodb_log_files_in_group = 2 xtrabackup: innodb_log_file_size = 50331648 >> log scanned up to (38314921) xtrabackup: Generating a list of tablespaces [01] Copying ./ibdata1 to /home/nilnandan/backup/2014-12-09_10-22-24/ibdata1 [01] ...done >> log scanned up to (38314921) xtrabackup: Creating suspend file '/home/nilnandan/backup/2014-12-09_10-22-24/xtrabackup_suspended_2' with pid '5654' 141209 10:22:26 innobackupex: Continuing after ibbackup has suspended 141209 10:22:26 innobackupex: Executing LOCK TABLES FOR BACKUP... 141209 10:22:26 innobackupex: Backup tables lock acquired 141209 10:22:26 innobackupex: Starting to backup non-InnoDB tables and files innobackupex: in subdirectories of '/var/lib/mysql/' innobackupex: Backing up file '/var/lib/mysql//nil/db.opt' innobackupex: Backing up file '/var/lib/mysql//nil/test.frm' 141209 10:22:26 innobackupex: Finished backing up non-InnoDB tables and files 141209 10:22:26 innobackupex: Executing LOCK BINLOG FOR BACKUP... >> log scanned up to (38314921) 141209 10:22:26 innobackupex: Executing FLUSH ENGINE LOGS... 141209 10:22:26 innobackupex: Waiting for log copying to finish xtrabackup: The latest check point (for incremental): '38314921' xtrabackup: Stopping log copying thread. .>> log scanned up to (38314921) xtrabackup: Creating suspend file '/home/nilnandan/backup/2014-12-09_10-22-24/xtrabackup_log_copied' with pid '5654' xtrabackup: Transaction log of lsn (38314921) to (38314921) was copied. 141209 10:22:27 innobackupex: Executing UNLOCK BINLOG 141209 10:22:27 innobackupex: Executing UNLOCK TABLES 141209 10:22:27 innobackupex: All tables unlocked innobackupex: Backup created in directory '/home/nilnandan/backup/2014-12-09_10-22-24' 141209 10:22:27 innobackupex: Connection to database server closed 141209 10:22:27 innobackupex: completed OK! nilnandan@Dell-XPS:~$ root@Dell-XPS:/home/nilnandan/backup/2014-12-09_10-22-24# ll total 26692 drwxr-xr-x 3 root root 4096 Dec 9 10:22 ./ drwxrwxr-x 4 nilnandan nilnandan 4096 Dec 9 10:22 ../ -rw-r--r-- 1 root root 358 Dec 9 10:22 backup-my.cnf -rw-r----- 1 root root 27262976 Dec 9 10:22 ibdata1 drwxr-xr-x 2 root root 4096 Dec 9 10:22 nil/ -rw-r----- 1 root root 91 Dec 9 10:22 xtrabackup_checkpoints -rw-r--r-- 1 root root 542 Dec 9 10:22 xtrabackup_info -rw-r----- 1 root root 2560 Dec 9 10:22 xtrabackup_logfile root@Dell-XPS:/home/nilnandan/backup/2014-12-09_10-22-24# After running --apply log nilnandan@Dell-XPS:~$ sudo innobackupex --apply-log /home/nilnandan/backup/2014-12-09_10-22-24 ... InnoDB: Restoring possible half-written data pages InnoDB: from the doublewrite buffer... InnoDB: Table mysql/innodb_index_stats in the InnoDB data dictionary has tablespace id 2, but tablespace with that id or name does not exist. Have you deleted or moved .ibd files? This may also be a table created with CREATE TEMPORARY TABLE whose .ibd and .frm files MySQL automatically removed, but the table still exists in the InnoDB internal data dictionary. InnoDB: It will be removed from the data dictionary. InnoDB: Please refer to InnoDB: http://dev.mysql.com/doc/refman/5.6/en/innodb-troubleshooting-datadict.html InnoDB: for how to resolve the issue. InnoDB: Table mysql/innodb_table_stats in the InnoDB data dictionary has tablespace id 1, but tablespace with that id or name does not exist. Have you deleted or moved .ibd files? This may also be a table created with CREATE TEMPORARY TABLE whose .ibd and .frm files MySQL automatically removed, but the table still exists in the InnoDB internal data dictionary. InnoDB: It will be removed from the data dictionary. InnoDB: Please refer to InnoDB: http://dev.mysql.com/doc/refman/5.6/en/innodb-troubleshooting-datadict.html InnoDB: for how to resolve the issue. InnoDB: Table mysql/slave_master_info in the InnoDB data dictionary has tablespace id 4, but tablespace with that id or name does not exist. Have you deleted or moved .ibd files? This may also be a table created with CREATE TEMPORARY TABLE whose .ibd and .frm files MySQL automatically removed, but the table still exists in the InnoDB internal data dictionary. InnoDB: It will be removed from the data dictionary. InnoDB: Please refer to ... xtrabackup: starting shutdown with innodb_fast_shutdown = 1 InnoDB: FTS optimize thread exiting. InnoDB: Starting shutdown... InnoDB: Shutdown completed; log sequence number 38330977 141209 10:23:32 innobackupex: Restarting xtrabackup with command: xtrabackup --defaults-file="/home/nilnandan/backup/2014-12-09_10-22-24/backup-my.cnf" --defaults-group="mysqld" --prepare --target-dir=/home/nilnandan/backup/2014-12-09_10-22-24 for creating ib_logfile* xtrabackup version 2.2.6 based on MySQL server 5.6.21 Linux (x86_64) (revision id: ) xtrabackup: cd to /home/nilnandan/backup/2014-12-09_10-22-24 xtrabackup: This target seems to be already prepared. xtrabackup: notice: xtrabackup_logfile was already used to '--prepare'. xtrabackup: using the following InnoDB configuration for recovery: xtrabackup: innodb_data_home_dir = ./ xtrabackup: innodb_data_file_path = ibdata1:12M:autoextend xtrabackup: innodb_log_group_home_dir = ./ xtrabackup: innodb_log_files_in_group = 2 xtrabackup: innodb_log_file_size = 50331648 xtrabackup: using the following InnoDB configuration for recovery: xtrabackup: innodb_data_home_dir = ./ xtrabackup: innodb_data_file_path = ibdata1:12M:autoextend xtrabackup: innodb_log_group_home_dir = ./ xtrabackup: innodb_log_files_in_group = 2 xtrabackup: innodb_log_file_size = 50331648 xtrabackup: Starting InnoDB instance for recovery. xtrabackup: Using 104857600 bytes for buffer pool (set by --use-memory parameter) InnoDB: Using atomics to ref count buffer pool pages InnoDB: The InnoDB memory heap is disabled InnoDB: Mutexes and rw_locks use GCC atomic builtins InnoDB: Memory barrier is not used InnoDB: Compressed tables use zlib 1.2.8 InnoDB: Using CPU crc32 instructions InnoDB: Initializing buffer pool, size = 100.0M InnoDB: Completed initialization of buffer pool InnoDB: Setting log file ./ib_logfile101 size to 48 MB InnoDB: Setting log file ./ib_logfile1 size to 48 MB InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0 InnoDB: New log files created, LSN=38330977 InnoDB: Highest supported file format is Barracuda. InnoDB: 128 rollback segment(s) are active. InnoDB: Waiting for purge to start InnoDB: 5.6.21 started; log sequence number 38331404 [notice (again)] If you use binary log and don't use any hack of group commit, the binary log position seems to be: xtrabackup: starting shutdown with innodb_fast_shutdown = 1 InnoDB: FTS optimize thread exiting. InnoDB: Starting shutdown... InnoDB: Shutdown completed; log sequence number 38331453 141209 10:23:34 innobackupex: completed OK! nilnandan@Dell-XPS:~$ root@Dell-XPS:/home/nilnandan/backup/2014-12-09_10-22-24# ll total 127060 drwxr-xr-x 3 root root 4096 Dec 9 10:23 ./ drwxrwxr-x 4 nilnandan nilnandan 4096 Dec 9 10:22 ../ -rw-r--r-- 1 root root 358 Dec 9 10:22 backup-my.cnf -rw-r----- 1 root root 27262976 Dec 9 10:23 ibdata1 -rw-r--r-- 1 root root 50331648 Dec 9 10:23 ib_logfile0 -rw-r--r-- 1 root root 50331648 Dec 9 10:23 ib_logfile1 drwxr-xr-x 2 root root 4096 Dec 9 10:22 nil/ -rw-r----- 1 root root 91 Dec 9 10:23 xtrabackup_checkpoints -rw-r--r-- 1 root root 542 Dec 9 10:22 xtrabackup_info -rw-r----- 1 root root 2097152 Dec 9 10:23 xtrabackup_logfile root@Dell-XPS:/home/nilnandan/backup/2014-12-09_10-22-24# ^^ here, I'm not seeing other databases.