I have again tried to run sysbench on the particular database for running transactions and meanwhile try to take backup of that DB and check but unable to reproduce the issue. I have also tried to run sysbench on one db and take backup of other db but still the result is same. I think, its better if you can provide the test case. nilnandan@Dell-XPS:~$ sysbench --test=/usr/share/doc/sysbench/tests/db/oltp.lua --oltp-table-size=100000 --oltp-test-mode=complex --oltp-read-only=off --num-threads=100 --max-time=120 --max-requests=0 --mysql-db=dbtest --mysql-user=root --mysql-password=root run sysbench 0.5: multi-threaded system evaluation benchmark Running the test with following options: Number of threads: 100 Random number generator seed is 0 and will be ignored Threads started! OLTP test statistics: queries performed: read: 2160928 write: 617394 other: 308698 total: 3087020 transactions: 154346 (1285.64 per sec.) read/write requests: 2778322 (23142.30 per sec.) other operations: 308698 (2571.33 per sec.) ignored errors: 6 (0.05 per sec.) reconnects: 0 (0.00 per sec.) General statistics: total time: 120.0539s total number of events: 154346 total time taken by event execution: 12002.7282s response time: min: 7.87ms avg: 77.77ms max: 458.67ms approx. 95 percentile: 143.40ms Threads fairness: events (avg/stddev): 1543.4600/60.97 execution time (avg/stddev): 120.0273/0.01 nilnandan@Dell-XPS:~$ nilnandan@Dell-XPS:~/Downloads/percona-xtrabackup-2.2.6-Linux-x86_64/bin$ sudo ./innobackupex --user=root --password=root --databases="dbtest" /home/nilnandan/backup InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy and Percona LLC and/or its affiliates 2009-2013. All Rights Reserved. This software is published under the GNU GENERAL PUBLIC LICENSE Version 2, June 1991. Get the latest version of Percona XtraBackup, documentation, and help resources: http://www.percona.com/xb/p 141229 13:58:42 innobackupex: Connecting to MySQL server with DSN 'dbi:mysql:;mysql_read_default_group=xtrabackup' as 'root' (using password: YES). 141229 13:58:42 innobackupex: Connected to MySQL server 141229 13:58:42 innobackupex: Executing a version check against the server... 141229 13:58:42 innobackupex: Done. 141229 13:58:42 innobackupex: Starting the backup operation IMPORTANT: Please check that the backup run completes successfully. At the end of a successful backup run innobackupex prints "completed OK!". innobackupex: Using server version 5.6.21-70.1 innobackupex: Created backup directory /home/nilnandan/backup/2014-12-29_13-58-42 141229 13:58:42 innobackupex: Starting ibbackup with command: xtrabackup --defaults-group="mysqld" --backup --suspend-at-end --target-dir=/home/nilnandan/backup/2014-12-29_13-58-42 --innodb_log_file_size="50331648" --innodb_data_file_path="ibdata1:12M:autoextend" --tmpdir=/tmp --extra-lsndir='/tmp' --databases='dbtest' innobackupex: Waiting for ibbackup (pid=9854) to suspend innobackupex: Suspend file '/home/nilnandan/backup/2014-12-29_13-58-42/xtrabackup_suspended_2' xtrabackup version 2.2.7 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 (805056420) xtrabackup: Generating a list of tablespaces [01] Copying ./ibdata1 to /home/nilnandan/backup/2014-12-29_13-58-42/ibdata1 >> log scanned up to (806894408) >> log scanned up to (808433338) >> log scanned up to (809856275) [01] ...done [01] Copying ./dbtest/sbtest1.ibd to /home/nilnandan/backup/2014-12-29_13-58-42/dbtest/sbtest1.ibd >> log scanned up to (811778727) [01] ...done xtrabackup: Creating suspend file '/home/nilnandan/backup/2014-12-29_13-58-42/xtrabackup_suspended_2' with pid '9855' >> log scanned up to (813319556) 141229 13:58:49 innobackupex: Continuing after ibbackup has suspended 141229 13:58:49 innobackupex: Executing LOCK TABLES FOR BACKUP... 141229 13:58:49 innobackupex: Backup tables lock acquired 141229 13:58:49 innobackupex: Starting to backup non-InnoDB tables and files innobackupex: in subdirectories of '/var/lib/mysql/' innobackupex: Backing up file '/var/lib/mysql//dbtest/sbtest1.frm' innobackupex: Backing up file '/var/lib/mysql//dbtest/db.opt' 141229 13:58:49 innobackupex: Finished backing up non-InnoDB tables and files 141229 13:58:49 innobackupex: Executing LOCK BINLOG FOR BACKUP... 141229 13:58:49 innobackupex: Executing FLUSH ENGINE LOGS... 141229 13:58:49 innobackupex: Waiting for log copying to finish xtrabackup: The latest check point (for incremental): '781213083' xtrabackup: Stopping log copying thread. .>> log scanned up to (814789209) xtrabackup: Creating suspend file '/home/nilnandan/backup/2014-12-29_13-58-42/xtrabackup_log_copied' with pid '9855' xtrabackup: Transaction log of lsn (769770926) to (814789209) was copied. 141229 13:58:50 innobackupex: Executing UNLOCK BINLOG 141229 13:58:50 innobackupex: Executing UNLOCK TABLES 141229 13:58:50 innobackupex: All tables unlocked innobackupex: Backup created in directory '/home/nilnandan/backup/2014-12-29_13-58-42' 141229 13:58:50 innobackupex: Connection to database server closed 141229 13:58:50 innobackupex: completed OK! nilnandan@Dell-XPS:~/Downloads/percona-xtrabackup-2.2.6-Linux-x86_64/bin$ After running --apply-log, root@Dell-XPS:/home/nilnandan/backup# ls -al 2014-12-29_13-58-42/ total 291200 drwxr-xr-x 3 root root 4096 Dec 29 14:00 . drwx------ 6 nilnandan nilnandan 4096 Dec 29 13:58 .. -rw-r--r-- 1 root root 358 Dec 29 13:58 backup-my.cnf drwx------ 2 root root 4096 Dec 29 13:58 dbtest -rw-r----- 1 root root 146800640 Dec 29 14:00 ibdata1 -rw-r--r-- 1 root root 50331648 Dec 29 14:00 ib_logfile0 -rw-r--r-- 1 root root 50331648 Dec 29 14:00 ib_logfile1 -rw-r----- 1 root root 93 Dec 29 14:00 xtrabackup_checkpoints -rw-r--r-- 1 root root 546 Dec 29 13:58 xtrabackup_info -rw-r----- 1 root root 50642944 Dec 29 14:00 xtrabackup_logfile root@Dell-XPS:/home/nilnandan/backup#