I got this error after upgrading to 0.55.1, Debian 9 Stretch and Python 3.6.
Need help to overcome this error. No homeassistant.db is created and not many automation scripts are working since no recorder or history is available.
Basically run this install:
sudo apt-get install libsqlite3-dev
Now in the downloaded python source rebuild and install python with the following command:
./configure --enable-loadable-sqlite-extensions && make && sudo make install
After doing this I reinstalled homeassisant and the error was gone