ls -a doesn't find sqlite DB file although locate does

Can anyone explain this? I have created a test database in sqlite3. I can locate it with the locate command, but 'ls -a' doesn't acknowledge its existence. I tried using sudo in case it was a permissions problem and that didn't work, so as a last resort I switched to root, but 'ls -a' still couldn't see it. (I've abbreviated the file paths for clarity.)

root@mycomputer:/.../scratches# locate test.db
/.../scratches/test.db    
root@mycomputer:/.../scratches# ls -a /.../test.db    
ls: cannot access /.../scratches/test.db: No such file or directory

Am I missing something obvious?

PS: OS is Ubuntu 12.04