I’m using XtraBackup 1.6.3. (I do realize there is a new version just out.) I’m also using the streaming option to create a gzipped archive of my backup via InnoBackupEx. When I recover the archive, I have an interesting issue. The ibdata* files get extracted directly into my /var/lib/mysql directory. However, on my server, they are located in /var/lib/mysql/innodb. Interestingly, to run the --apply-log step, I have to leave the files in /var/lib/mysql, then move them to /var/lib/mysql/innodb prior to starting my MySQL instance.
Would this be considered a bug of some sort? It certainly makes recovering from a backup less than straightforward. It took me a while to figure it out. Before that, I would recover and find that my database was unreadable.