Metaphlan4 species not included in Humann3.5 output?

Microbial community profiling HUMAnN
1

Hi! I noticed that in the Humann3.5 pathway abundance output, only a subset of the Metaphlan4 species are present as contributors to pathway abundance (i.e. SGB species and some others are missing in the pathway file). Is this supposed to be the case? If so, is the Humann3.5 output not representative of all the species present based on the Metaphlan4 genomes?

Thank you,
Brandi

2

That’s right - HUMAnN 3.5 will profile the subset of species that it recognizes from MetaPhlAn 4.0 output, but species that are new to MetaPhlAn 4.0 (especially uSGBs) will be skipped. HUMAnN 4.0 is in development and will again fully cover the MetaPhlAn species, but we released HUMAnN 3.5 in the interim to maximize compatibility between the software versions.

3

Hi,
We are also interested in running Humann on metaphlan 4 output. Can Humann 3.6 be run directly on the metaphlan 4 mpa_vJan21_CHOCOPhlAnSGB_202103 db?
Is the development version of Humann 4 available?
Can you share a time estimate for Humann 4 official release?
Thank you,
Ilya.

4

HUMAnN 3.6 can be run with MetaPhlAn 4 databases - it will match as many of the SGBs as it can based on their species-level taxonomy. A development version of HUMAnN 4 is close - I would expect to see it in the next couple of months.

5

really lookding forward to the new version at the SGBlevel!

6

Hello,

I RAN Humann 3.5 with the vOct22_CHOCOPhlAnSGB database and also received the following error message

“File “/apps/humann/3.5/bin/humann”, line 10, in
sys.exit(main())
File “/apps/humann/3.5/lib/python3.10/site-packages/humann/humann.py”, line 979, in main
custom_database = prescreen.create_custom_database(config.nucleotide_database, bug_file)
File “/apps/humann/3.5/lib/python3.10/site-packages/humann/search/prescreen.py”, line 215, in create_custom_database
config.metaphlan_v3_db_version+” or “+metaphlan_v4_db_version+” . Please update your version of MetaPhlAn to at least
v3.0."
NameError: name ‘metaphlan_v4_db_version’ is not defined"

Is Huamnn 3.5 compatible with the new database? If not, what are the options to work around it? Thanks very much!

7

The different HUMAnN 3.5+ point releases have been build to be compatible with successive versions of MetaPhlAn 4, so if you’re using a more recent MetaPhlAn 4 you probably need the newest HUMAnN 3.X.

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