Removed species appear as empty columns in the HOG files

[davidemms]

Steps to reproduce:

1. Run OrthoFinder on the ExampleData up to the orthogroups:
   python orthofinder.py -f ExampleData/ -og
2. Comment out species 1 & 3 in ExampleData/OrthoFinder/Results_Nov06/WorkingDirectory/SpeciesIDs.txt
3. Run OrthoFinder again adding two extra species:
   python orthofinder.py -f ExtraSpecies/ -b ExampleData/OrthoFinder/Results_Nov06/

Outcome:
There are columns in Phylogenetic_Hierarchical_Orthogroups/N0.tsv for all 6 species, including the two that were excluded.

Expected outcome:
There should only be columns in Phylogenetic_Hierarchical_Orthogroups/N0.tsv for the species included in the analysis (species 0, 2, 4 & 5) not the ones that were excluded ("1: Mycoplasma_gallisepticum.faa" & "3: Mycoplasma_hyopneumoniae.faa")