I've run into an issue getting the Matcher to work correctly. I have attached a log file with the error I am receiving (In this particular case I ran 3.4, but the error is the same for 3.5). The specific error is below:
ERROR: olditer != target_restype_index_map_.end()
ERROR:: Exit from: src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.cc line: 677
Any help would be greatly appreciated and if additional information is needed I would be glad to provide it.