The 10gen/jepsen's default branch was changed to track https://github.com/jepsen-io/mongodb/tree/master/, which doesn't have a jepsen/ subdirectory since MongoDB's Jepsen tests were split out from the jepsen-io/jepsen repository. The "do jepsen setup" function should check out the mongodb-master-linearizable-2 before trying to change to the jepsen/ subdirectory to ensure it is using the expected version of the tests.

[2017/03/31 21:09:07.491] Running command 'shell.exec' in "do jepsen setup" (step 2.1 of 3)
[2017/03/31 21:09:07.494] Cloning into 'jepsen'...
[2017/03/31 21:09:09.304] sh: 3: cd: can't cd to jepsen/jepsen
[2017/03/31 21:09:09.304] Command failed: exit status 2