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mptrsen / Orthograph

Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models
GNU General Public License v3.0
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--cog-list-file #38

Open CristianBezaBeza opened 2 years ago

CristianBezaBeza commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

mptrsen commented 2 years ago

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