Humann_regroup_table lost uniref90_ko,uniref90_levelec

Microbial community profiling HUMAnN
1

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Hello,

I used the command humann_regroup_table --input ${genefamilies} -g uniref90_ko -u N -p N -o ${meta.id}.KO.txt and encountered the error: humann_regroup_table: error: argument -g/--groups: invalid choice: 'uniref90_ko' (choose from 'uniref90_rxn', 'uniref50_rxn'). However, my previous environment worked fine. As shown in the image, after updating HUMAnN, the -g option in humann_regroup_table --help only has two choices: uniref90_rxn and uniref50_rxn, as shown in the image below. What should I do?

Here are the databases I selected:

  • humann_nucleotide_db = "/ssd1/metagenome_data/humann/chocophlan_v31_201901/"
  • humann_protein_db = "/ssd1/metagenome_data/humann/uniref90_v201901_ec_filtered/"
  • humann_utility_mapping_db = "/ssd1/metagenome_data/humann/mapping_v201901/"
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2

It looks like your utility mapping database isn’t complete / has never been upgraded. The RXN maps are bundled with HUMAnN, so you’re seeing those as the only default options. Searching here for how to update the utility mapping database will resolve this.