At times when closing Grafana with a kill command SqLite can get corrupted.
This is the one liner that saves the day:
# echo ".dump" | sqlite3 grafana.db | sqlite3 grafana_new.db
This will load, clean, validate and then dump the db file in a new db file.
Then simply copy the new grafana_new.db as the new grafana.db and restart Grafana.