I’m sorry if there was a previous post with this problem, but I couldn’t find any that could solve the issue.
I performed humann on my fasta file in Humann3, which generated the genefamilies.tsv, pathabundance.tsv and pathcoverage.tsv files as expected.
humann -i input_file.fasta -o humann_output_folder --search-mode uniref90 --nucleotide-database chocophlan_v201901b -protein-database uniref90_diamond
I wanted to run the humann_regroup_table command to compute KOs from the genefamilies, but the argument for --group uniref90_ko isn’t available.
- I’ve successfully download the humann_database: humann_databases --download utility_mapping full $DIR
However, I got an error that state ‘Unable to write on the Humann config file’. I presume that this may be due to the permission to read/write in selected folders?
- How can I provide the file directly from the humann_database that I’ve downloaded (or if there is any mapping/reformatting file available) to perform the regroup as a workaround to the above to compute KOs?
Any advice is much appreciated. Thank you!