Rocket.Chat Version: 0.54.2
Running Instances: 1
DB Replicaset OpLog: Disabled
Node Version: 4.8.1

I had the same problem like #1149.

I followed kalebwalton solution step to solve the problem.

use mydb
db.users.find(
{"username":"kwalton"}
) <-- just to make sure the user existed
db.users.remove(
{"username":"kwalton"}
) <-- deletes the user
Then I re-logged in to Rocket.Chat and it worked. But I ran into another issue where I couldn't direct message someone, so I went back into mongo and:
use mydb
db.rocketchat_subscription.find({"name":"kwalton"}) <-- copied the rid value for the person and my conversation
db.rocketchat_subscription.remove({"name":"kwalton"}) <-- deletes my subscriptions
db.rocketchat_room.find({"_id":""}) <-- just to make sure the room exists
db.rocketchat_room.remove({"_id":""}) <-- remove the room
Also found any other rooms that matched the other person and I:
db.rocketchat_room.find({"usernames" : [ "theotherperson", "kwalton" ]})
db.rocketchat_room.remove({"usernames" : [ "theotherperson", "kwalton" ]}) <-- removed all rooms between us, appeared to be a dupe in there causing trouble

But now I have an other problem.
Now it says "No user with username was found!" when trying to access the direct message.