inferencing pipeline results change between older and new versions of ontopilot

[jdeck88]

I get different reasoning results using the inferencing pipeline feature from an older version of ontopilot (see elk_pipeline branch) versus the most recent (master branch). With the master branch i'm not getting it to infer any present traits as expected but things work as expected using the elk_pipeline branch. Interestingly, i'm able to reason OK using the ontology for vertebrate traits using OVT on the master branch. However, OVT does not rely on counts to make assertions and only uses subclass relationships on what we describe as present traits.
I've attached a zip file to this question that contains three files: 1) a sample .ttl file with instance data, 2) a reasoner.conf file, and 3) a test.sh script to run it.

ontopilot_question.zip