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Published 20 hours ago • verified publisher icon mptrsen

--cog-list-file

Open CristianBezaBeza opened this issue 2 years ago • 3 comments

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?

CristianBezaBeza avatar May 05 '22 16:05 CristianBezaBeza

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?

mptrsen avatar May 06 '22 13:05 mptrsen

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

CristianBezaBeza avatar May 06 '22 14:05 CristianBezaBeza

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

mptrsen avatar May 06 '22 14:05 mptrsen