I tried stopping bitcoind using bitcoin-cli stop and got the following error.

bitcoin-cli stop
error: Could not locate RPC credentials. No authentication cookie could be found, and RPC password is not set.  See -rpcpassword and -stdinrpcpass.  Configuration file: (/home/user/.bitcoin/bitcoin.conf)

I confirmed that bitcoind is running (using ps -A).

ps -A | grep bitcoind
643 pts/0    00:17:23 bitcoind

bitcoind was started in a datadir on the usb storage. I can kill the process but i want to shut it down in a correct way.