Backup the InnoDB data and log files - located in /var/lib/mysql/ - to /data/backups/mysql/ (destination). Then, prepare the backup files to be ready to restore or use (make the data files consistent).
In the second --prepare step, you should see InnoDB print messages similar to Logfile./ib_logfile0didnotexist:newtobecreated, followed by a line indicating the log file was created (creating new logs is the purpose of the second preparation).
This documentation is developed in Launchpad as part of the Percona XtraBackup 1.6.
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