Hello, it seems to me you have to simply define your proteins as a list. This means you choose the id's that you use for each one (accessions, GI's, your own numbering). The same goes for the genome-id - just use an identifier for the organism that the protein comes from. Have a look also at this answer to a similar question:

https://www.biostars.org/p/126011/#126241

Hope this clears things up a bit!

Ivan

Thanks Ivan! It helps a lot!

Hi Bei and Ivan,

I am also having the same problem. According to your discussion and this discussion:https://www.biostars.org/p/126011/#126241

I tried to created the attached csv file. But getting error like: 

command: COGmakehash -i=protein_id_falciparum.csv -o=./BLASTconv -s="," -n=1

output: Can't open output file ./BLASTconv/hash.csv

This error is consistent. What do you think my csv file that I am providing is good or bad?

Any suggestion will be warmly appreciated.

Best Regards

Zillur