You're right, nothing about that looks wrong. There must be something else hidden in the details of the rest of the netlist that is confusing things.
This will probably require the full netlist to diagnose the issue. If there is sensitivity involved and you can't share the netlist on the public group, please contact the team via the
sandia.gov contact address on the web site, and we could arrange a way of communicating with you privately. This "Data not in directory" error is so obscure and hard to trip that there's almost no way to diagnose it without access to an actual full test case that trips it.
Whatever the error in the netlist is, it should be getting caught before the code ever hits that unhelpful error condition, so this is something we ought to work on and get fixed.