Code:
total 172
drwxr-xr-x 2 root root 4096 2012-10-04 23:04 bin
drwxr-xr-x 3 root root 4096 2013-05-17 23:57 boot
drwxr-xr-x 2 root root 4096 2011-05-18 19:22 cdrom
drwxr-xr-x 17 root root 3760 2013-05-28 08:23 dev
drwxr-xr-x 153 root root 12288 2013-05-28 08:23 etc
drwxr-xr-x 4 root root 4096 2010-04-23 12:11 home
lrwxrwxrwx 1 root root 33 2013-05-17 23:57 initrd.img -> boot/initrd.img-2.6.32-47-generic
lrwxrwxrwx 1 root root 33 2013-03-23 19:06 initrd.img.old -> boot/initrd.img-2.6.32-46-generic
drwxr-xr-x 22 root root 16384 2013-04-10 16:01 lib
drwx------ 2 root root 16384 2011-05-18 19:20 lost+found
drwxr-xr-x 7 root root 4096 2013-05-23 08:54 media
drwxr-xr-x 3 root root 4096 2012-12-20 14:39 mnt
drwxr-xr-x 8 root root 4096 2013-05-20 16:50 opt
dr-xr-xr-x 151 root root 0 2013-05-28 08:23 proc
drwx------ 16 root root 4096 2013-04-30 21:17 root
drwxr-xr-x 2 root root 4096 2013-04-10 16:01 sbin
drwxr-xr-x 2 root root 4096 2009-12-05 22:55 selinux
drwxr-xr-x 3 root root 4096 2011-10-19 00:47 srv
drwxr-xr-x 12 root root 0 2013-05-28 08:23 sys
drwxrwxrwt 18 root root 73728 2013-05-28 15:05 tmp
drwxr-xr-x 13 root root 4096 2011-05-27 11:59 usr
drwxr-xr-x 15 root root 4096 2011-02-11 14:20 var
lrwxrwxrwx 1 root root 30 2013-05-17 23:57 vmlinuz -> boot/vmlinuz-2.6.32-47-generic
lrwxrwxrwx 1 root root 30 2013-03-23 19:06 vmlinuz.old -> boot/vmlinuz-2.6.32-46-generic
The rights for /opt still exist but I guess it has something to do about disc corruption as Kovid mentioned, although SMART tests are ok. Could there be a conflict between calibre libraries and mime-database?
Some other Ubuntu 10.04.4 user got the same issue but couldn't get proper answers that's why I thought it was more of an upgrade issue
http://askubuntu.com/questions/29272...-mime-database
Thanks a lot for your thoughts.