Missing Orthologues

[rustem-musaev]

Hello!

I'm trying to run this command:

aureme --run=microalgae --cmd="orthology_based"

The OrthoFinder step finished successfully, with .tsv files containing orthologues and genes in the respective folders. However, the process stops when AuReMe attempts to create a draft model for my organism:

...
Orthogroups have been written to tab-delimited files:
   /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/OrthoFinder/Results_Dec15/Orthogroups/Orthogroups.tsv
   /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/OrthoFinder/Results_Dec15/Orthogroups/Orthogroups.txt (OrthoMCL format)
   /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/OrthoFinder/Results_Dec15/Orthogroups/Orthogroups_UnassignedGenes.tsv
Sequences for orthogroups:
   /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/OrthoFinder/Results_Dec15/Orthogroup_Sequences/


Gene trees:
   /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/OrthoFinder/Results_Dec15/Gene_Trees/

Rooted species tree:
   /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/OrthoFinder/Results_Dec15/Species_Tree/SpeciesTree_rooted.txt

Species-by-species orthologues directory:
   /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/OrthoFinder/Results_Dec15/Orthologues/

Orthogroup statistics:
   Statistics_PerSpecies.tsv   Statistics_Overall.tsv   Orthogroups_SpeciesOverlaps.tsv

OrthoFinder assigned 1594 genes (4.8% of total) to 485 orthogroups. Fifty percent of all genes were in orthogroups with 1 or more genes (G50 was 1) and were contained in the largest 15643 orthogroups (O50 was 15643). There were 485 orthogroups with all species present and 214 of these consisted entirely of single-copy genes.

------>RUNNING STEP : Creating models from /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/Orthologues
Parsing Orthofinder output /shared/microalgae/orthology_based_reconstruction/orthofinder_wd/Orthologues
Start sbml creation...
*Extracting orthologues data to create sbml of microalgae from mixo
	Sbml of mixo contains 1924/2394 reactions with genes assocation
	No reaction added from mixo to microalgae because of missing orthologues

I've tried to do something with the tsv files, I thought maybe the fact that sometimes several genes separated by a comma are assigned to one orthologue might be a problem, so I divided such entries into separate lines, but it still didn't work. Also, I've edited the database variable in the config.txt file because most of the reaction IDs in the template model are from the BIGG database. I'm stumped, what should I do? Thanks in advance!