My Ubuntu server is installed on hard drive with very simple partitioning

/dev/sdd1   *           1        1824    14647296   83  Linux

/dev/sdd2            1824        3283    11718656   83  Linux

/dev/sdd3            3283        4864    12702720   82  Linux swap / Solaris

So about 14GB is allocated for / and about 12GB for /home. The rest is swap.

Today I noticed when I login I got a warning that running out of space. df shows the following

Filesystem            Size  Used Avail Use% Mounted on

/dev/sdd1              14G   13G  619M  96% /

none                  2.9G  260K  2.9G   1% /dev

none                  2.9G     0  2.9G   0% /dev/shm

none                  2.9G  852K  2.9G   1% /var/run

none                  2.9G     0  2.9G   0% /var/lock

none                  2.9G     0  2.9G   0% /lib/init/rw

/dev/sdd2              12G  2.6G  8.0G  25% /home

At this point I am trying to understand what eats 13G on my root partition. du shows the following output

$ sudo du -hxL --exclude="/home" --max-depth=1 / # excluding home because

                                                  it's other partition



0       /sys

4.0K    /selinux

4.0K    /mnt

447M    /lib

4.0K    /opt

1.9G    /usr

64M     /etc

447M    /lib64

31M     /boot

8.2M    /sbin

8.0K    /man

48K     /root

358M    /var

0       /proc

0       /dev

4.0K    /srv

16K     /lost+found

28K     /tmp

12M     /bin

3.2G    /

parted

Disk /dev/sdd: 40.0GB

Sector size (logical/physical): 512B/512B

Partition Table: msdos



Number  Start   End     Size    Type     File system     Flags

 1      1049kB  15.0GB  15.0GB  primary  ext4            boot

 2      15.0GB  27.0GB  12.0GB  primary  ext4

 3      27.0GB  40.0GB  13.0GB  primary  linux-swap(v1)

The sum is far not 13G, in fact it's around 5G. So what exactly takes space on my root partition?