Sqlite SQLITE_MISUSE error in node.js script

You've got a race condition; it's possible that your last query (whose callback closes the connection) will finish before one of the earlier queries did, and that will, needless to say, hose the earlier query. You need to rework your code so that the last query to finish, rather than the last query to start, closes the connection (e.g set a counter to the number of queries and have each query decrement it when it finishes. The one that decrements it to zero closes the connection).

You might also want to look at the serialize method that's available on database objects. Right now your initialization queries are all independent of each other, but if you started using foreign-key constraints you'd have trouble if the referenced table hadn't been created yet, so you'd need to force the order of execution.