I have been trying to run OMA standalone using a few genomes downloaded from the OMA browser and then adding a couple of my custom genomes. All the steps of OMA standalone including All-vs-All computations, pairwise orthologs etc have successfully finished. However, I have consistently faced the same error with the final step of generating and storing HOGs for these genomes.

Here is the error message that I get despite trying to run OMA on different machines:

    ********************************************************************************

    Storing results
    Traceback (most recent call last):
      File "/home/orthologs/OMA.2.4.1/bin/..//.venv/bin/warthogs.py", line 128, in <module>
        run_gethogs()
      File "/home/orthologs/OMA.2.4.1/bin/..//.venv/bin/warthogs.py", line 95, in run_gethogs
        Settings.check_consistency_argument()
      File "/home/orthologs/OMA.2.4.1/.venv/lib64/python3.6/site-packages/gethogs/settings.py", line 53, in check_consistency_argument
        cls.inputfile_handler = file_manager.inputfile_handler_factory()
      File "/home/orthologs/OMA.2.4.1/.venv/lib64/python3.6/site-packages/gethogs/file_manager.py", line 97, in inputfile_handler_factory
        return OmaStandaloneFiles(os.path.normpath(join(settings.Settings.pairwise_folder, '..')))
      File "/home/orthologs/OMA.2.4.1/.venv/lib64/python3.6/site-packages/gethogs/file_manager.py", line 44, in __init__
        for row in csv_reader:
    _csv.Error: field larger than field limit (131072)
    ********************************************************************************
    An error occured in bottom-up HOG computations:
    
     --- WARTHOGs:
    	- Start at 13:36 on 2020-12-08 
    	- Orthology relations folder:Output/PairwiseOrthologs (standalone format)
    	- Method use to merge HOGS: pair
    	- Output file: Output/HierarchicalGroups.orthoxml
    
    
    
    Error, (in GetHOGsBottomUp) failed to compute bottom-up hogs

Can somebody please help me with this error? 

Also is there a way to only run the HOG computation stage of the program without having to generate all the output files again?
Hi Gaurav, (hi Alberto)

I had a look at the problem and it turns out that there are some proteins with a huge number of crossreferences in the fasta header. The csv module has a limit on the length of each field, which is exceeded by these proteins.
The fix is quite simple, so you can actually do it yourself if you want. I also plan to release a new version of oma standalone within the next days that contains that fix (will be 2.4.2).

what you need to do is to include in `hog_bottom_up/gethogs/file_manager.py` right after the import lines:

    csv.field_size_limit(1<<20)

After this change, the analysis run through in a few minutes without further problems.

Thanks for pointing out the problem and good look with our analysis

Adrian
