--cog-list-file

[CristianBezaBeza]

I am trying to run Orthograph using a subset of COGs. I have tried to specify the cog-list in the config file and as an option in the command. However, Orthograph ignores this file; it does not give me an error message or anything. Do you have any advice?

[mptrsen]

Please make sure the IDs are actually present in your reference sets. Also make sure the COG list to be excluded is properly formatted (no Windows/Mac line breaks). Can you post a sample?

[CristianBezaBeza]

Thank you for the response Malte. This is the COG list I am providing to Orthograph
Calliphoridae_threshold_scos.txt

[mptrsen]

Please also post a sample of the COG table that you used to create the ortholog set. The identifiers have to match.