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This fixed the problem:
http://www.synchrosinteractive.com/blog/1-software/47-mongodb-repair-on-ubuntu
Apparently mongodb creates a lock file when the database crashes or something. Deleting that file and repairing mongodb fixes the problem:
Manually remove the lockfile: sudo rm /var/lib/mongodb/mongod.lock
Run the repair script: sudo -u mongodb mongod -f /etc/mongodb.conf —repair
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