No full uniref90 db in humann4

Microbial community profiling HUMAnN
1

I submitted a question on the forum:
Currently using humann version 4.0.0a1. While downloading the database, I noticed the available databases are as follows:

HUMAnN Databases ( database : build = location )
chocophlan : full = http://huttenhower.sph.harvard.edu/humann_data/chocophlan/chocophlan.v4_alpha.tar.gz
chocophlan : ec_filtered = http://huttenhower.sph.harvard.edu/humann_data/chocophlan/chocophlan_EC_FILTERED.v4_alpha.tar.gz
uniref : uniref90_ec_filtered_diamond = http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_ec_filtered/uniref90_annotated_v4_alpha_ec_filtered.tar.gz
utility_mapping : full = http://huttenhower.sph.harvard.edu/humann_data/full_mapping_v4_alpha.tar.gz

Among these, uniref only offers uniref90_ec_filtered_diamond. I noticed the tutorial recommends downloading uniref90_diamond, but it seems this is not valid for humann4.

Since the 2019 version is too old, but the current uniref90 is also a filtered version, is there a suitable full version of uniref90 for humann4?

2

Update on this issue:

I later checked the HUMAnN 4.0.0.alpha.1 release notes and confirmed that there is indeed no full version of UniRef90 available yet, only the filtered version (uniref90_ec_filtered_diamond). It seems we’ll need to wait for the official release to get the complete version.

New issue encountered:

When running humann, I’m getting the following error:

CRITICAL ERROR: Can not call software version for metaphlan

However, I’ve confirmed that metaphlan is working properly:

(biobakery) $ metaphlan -v
MetaPhlAn version 4.2.4 (21 Oct 2025)
Installed databases: mpa_vJan25_CHOCOPhlAnSGB_202503

My environment details:

  • Using a biobakery environment created with conda/mamba

  • MetaPhlAn database installed in the default mamba environment location

  • HUMAnN version: 4.0.0.alpha.1

  • MetaPhlAn version: 4.2.4

Does anyone know what might be causing this “Can not call software version for metaphlan” error? Could this be a compatibility issue between HUMAnN 4.0.0.alpha.1 and the latest MetaPhlAn 4.2.4?

Looking at the release notes, HUMAnN 4.0.0.alpha.1 requires MetaPhlAn 4.0 and a specific database version (mpa_vOct22_CHOCOPhlAnSGB_202403), but I have newer versions installed. Could this be the problem?

3

I get the same error. No full uniref90 db in humann4.

(HUMAnN4) [jialonghao@admin databases]$ humann_databases --download uniref uniref90_diamond HUMAnN4_database
ERROR: Please select an available build.
(HUMAnN4) [jialonghao@admin databases]$ humann_databases -help
usage: humann_databases [-h] [--available] [--download <database> <build> <install_location>] [--update-config {yes,no}]
                        [--database-location DATABASE_LOCATION]

HUMAnN Databases

options:
  -h, --help            show this help message and exit
  --available           print the available databases
  --download <database> <build> <install_location>
                        download the selected database to the install location
  --update-config {yes,no}
                        update the config file to set the new database as the default [DEFAULT: yes]
  --database-location DATABASE_LOCATION
                        location (local or remote) to pull the database
(HUMAnN4) [jialonghao@admin databases]$ humann_databases --available
HUMAnN Databases ( database : build = location )
chocophlan : full = http://huttenhower.sph.harvard.edu/humann_data/chocophlan/chocophlan.v4_alpha.tar.gz
chocophlan : ec_filtered = http://huttenhower.sph.harvard.edu/humann_data/chocophlan/chocophlan_EC_FILTERED.v4_alpha.tar.gz
uniref : uniref90_ec_filtered_diamond = http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_ec_filtered/uniref90_annotated_v4_alpha_ec_filtered.tar.gz
utility_mapping : full = http://huttenhower.sph.harvard.edu/humann_data/full_mapping_v4_alpha.tar.gz
(HUMAnN4) [jialonghao@admin databases]$ humann_databases --download uniref uniref90_ec_filtered_diamond HUMAnN4_database
Creating subdirectory to install database: /public/home/jialonghao/GMMdb/databases/HUMAnN4_database/uniref
Download URL: http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_ec_filtered/uniref90_annotated_v4_alpha_ec_filtered.tar.gz
0.87 GB         
Extracting: /public/home/jialonghao/GMMdb/databases/HUMAnN4_database/uniref90_annotated_v4_alpha_ec_filtered.tar.gz

Database installed: /public/home/jialonghao/GMMdb/databases/HUMAnN4_database/uniref

HUMAnN configuration file updated: database_folders : protein = /public/home/jialonghao/GMMdb/databases/HUMAnN4_database/uniref