When you run apt and have following errors:
E: Read error - read (5: Input/output error) E: The package lists or status file could not be parsed or opened.
This means that you are in serious trouble, it's not hopeless but serious.
This error is caused by apt having some problems reading some of its config files. Too bad apt can't say in which file the problem is, and what is the problem.
Obviously there is no single answer on how to fix it, here are some hints.
Remove package cache: apt-get clean. Will purge some stuff. Probably won't help but it is safe (yes rest of the commands aren't safe).
Remove package lists:
sudo rm -rf /var/lib/apt/lists sudo mkdir /var/lib/apt/lists sudo mkdir /var/lib/apt/lists/partial
Restore an old version of dpkg status files. This is the file, where all information on packages installed, is stored. Sometimes it is corrupted, however, it has automatic backups. The file is /var/lib/dpkg/status, first thing to try would be:
cp /var/lib/dpkg/status /var/lib/dpkg/status.broken cp /var/lib/dpkg/status.old /var/lib/dpkg/status
This will restore the previous version of this file, there are older ones in /var/backup/dpkg.status*, but probably try the next step first.
apt (or aptitue) also store its copy of dpkg state, with additional information (like which package was installed by the user, and which is as a dependency). This can also be corrupted, so:
cp /var/lib/apt/extended_states /var/lib/apt/extended_states.broken cp /var/backups/apt.extended_states.0 /var/lib/apt/extended_states
One of the reasons for corrupted files can be file-system or hard drive problems. If you reached this point please consider backing up your data, running fsck, and diagnosing you drive (probably in this order).
Some people reported success with manually editing status files.
There is also a very extensive list of commands that might help you with diagnosing problems with apt: https://help.ubuntu.com/community/PackageManagerTroubleshootingProcedure I wouldn't recommend running them without understanding though.