Matching tools and database versions

Microbial community profiling HUMAnN
1

Hi,

I’m new to BioBakery and I’m finding it a bit challenging to identify the correct and compatible versions of MetaPhlAn, HUMAnN, and their associated databases.

Could you share how you typically manage version compatibility? Is there a reference list or resource that outlines which versions work best together?

Thank you very much for your time and support!

Best,

Matthieu

3

Thanks @Gsmith535 for the comments. We have been monitoring this issue and are working on a software/database version compatibility table that we will post as a pinned comment soon. We’re also working on new MetaPhlAn and HUMAnN releases that will do a better job of checking/enforcing those requirements during install and at runtime.

1 Like
4

Thanks for the quick follow up, that would be super! I appreciate the effort you all are investing to develop these tools, manage databases, and document as changes occur.

5

Thanks a lot for your help.

6

Looking forward to thos software/database.
Thanks Eric

7

Hi Eric,
Any update on the software/database version compatibility table?
Many thanks for your time considering this request.

8

You can get a rough table as follows:

  for tag in 3.1.1 3.5 3.6.1 3.7 v3.8 v3.9 4.0.0.alpha.1 4.0.0.alpha.1-final ; do git checkout $tag ; cat humann/config.py | grep -e "metaphlan_v4_db_version\|metaphlan_v4_db_matching_uniref\|matching_uniref" | sed "s|^|$tag\t|g" ; done  > version_table
cat version_table


3.1.1   metaphlan_db_matching_uniref="v201901_v31"
3.1.1   matching_uniref="201901b"
3.5     metaphlan_v4_db_version="vJan21"
3.5     metaphlan_v3_db_matching_uniref="v201901_v31"
3.5     matching_uniref="201901b"
3.6.1   metaphlan_v4_db_version="vJan21"
3.6.1   metaphlan_v3_db_matching_uniref="v201901_v31"
3.6.1   matching_uniref="201901b"
3.7     metaphlan_v4_db_version="vOct22"
3.7     metaphlan_v3_db_matching_uniref="v201901_v31"
3.7     matching_uniref="201901b"
v3.8    metaphlan_v4_db_version="vOct22"
v3.8    metaphlan_v3_db_matching_uniref="v201901_v31"
v3.8    matching_uniref="201901b"
v3.9    metaphlan_v4_db_version="vJun23"
v3.9    metaphlan_v3_db_matching_uniref="v201901_v31"
v3.9    matching_uniref="201901b"
4.0.0.alpha.1   metaphlan_v4_db_version="vOct22"
4.0.0.alpha.1   metaphlan_v4_db_matching_uniref="SGB"
4.0.0.alpha.1   matching_uniref="2019_06"
4.0.0.alpha.1-final     metaphlan_v4_db_version="vOct22_CHOCOPhlAnSGB_202403"
4.0.0.alpha.1-final     metaphlan_v4_db_matching_uniref="SGB"
4.0.0.alpha.1-final     matching_uniref="2019_06"
9

Thank you @nickp60 it certainly helps.

What would further help is a consolidated list or matrix documenting the compatibility between HUMAnN software and database versions and MetaPhlAn software and database versions, covering both the officially paired versions and any validated backward‑compatible configurations.
This would help determine when MetaPhlAn results need to be reprocessed prior to running HUMAnN.

1 Like
10

100% agree. We moved to just supporting a handful of version sets and built containers for the working combos. Some notes about them here.