Dear Fawei,
I have no good idea what causes the error that you are facing. It might have caused by TreeTagger, but I am not sure.
The problem is (as the exercise state) that those ex-n examples are written for the fall school event, and no longer supported.
I would like to point you to official "step by step" tutorial of EOP; which will guide you to train a model, and also enable you to query T-H pairs one by one.
https://github.com/hltfbk/EOP-1.2.3/wiki/Step-by-Step-Tutorial(For example, step #5 shows you how to annotate a single pair, and steps needed to that are explained in full.)
This document, and the code within that, are essentially equivalent to the "old" document, but more up to date, and being maintained. Hope this "step by step tutorial" would be helpful for you.
Sincerely,
Gil