Rsync / Sqlite database

I think you want to try:

pragma integrity_check;

From the documentation:

This pragma does an integrity check of the entire database. The integrity_check pragma looks for out-of-order records, missing pages, malformed records, missing index entries, and UNIQUE and NOT NULL constraint errors. If the integrity_check pragma finds problems, strings are returned (as multiple rows with a single column per row) which describe the problems. [...]

See also the PRAGMA quick_check command which does most of the checking of PRAGMA integrity_check but runs much faster.

Aha, just stumbled across an article explaining this. Also Django have info on their NewbieMistakes page.

The solution is to make sure the directory containing the database file also has write access allowed to the process.

In my case, running this command fixed the problem:

sudo chown www-data .