Announcing HUMAnN 3.6 (Critical Update)

Microbial community profiling HUMAnN
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We recently discovered a critical bug in DIAMOND 0.9.36 (as used by HUMAnN 3.0-3.5) that results in substantial loss of high-quality alignments during the translated phase of HUMAnN’s tiered search. DIAMOND’s developer has since confirmed that this bug was present in DIAMOND 0.9.33-0.9.36 but has been corrected in DIAMOND 2.0+. The bug did not affect our benchmarking of HUMAnN 3 in the bioBakery 3 paper (at that time, HUMAnN 3 used DIAMOND 0.9.24) but more recent analyses may have been affected. HUMAnN 3.6 updates the software to use DIAMOND 2.0.15+ for translated search, thus resolving this issue. All HUMAnN 3 users should upgrade to this version and may wish to consider reprofiling affected samples.

What has changed in HUMAnN 3.6:

  • HUMAnN 3.6 now requires DIAMOND 2.0.15+ for translated alignment.
  • This change substantially increases the number of reads that can be mapped to UniRef90 (or UniRef50) during translated search after those reads fail to map to a microbial pangenome.
  • This change restores the mapping rate and overall performance of HUMAnN’s translated search as observed in our original benchmarking for the bioBakery 3 paper.

What has NOT changed in HUMAnN 3.6:

  • HUMAnN 3.6 is a software/dependency update only. If you are upgrading from HUMAnN 3.1+ then you will not need to update your HUMAnN databases to use this version of the software (DIAMOND 0.9.36 and DIAMOND 2.0+ use the same database format).
  • This change does not affect taxonomic profiling with MetaPhlAn or the assignment of reads to species pangenomes (and thus species-stratified function abundances).
  • HUMAnN 3.6 remains compatible with MetaPhlAn 3.0+ and MetaPhlAn 4.0 (you can upgrade to HUMAnN 3.6 without upgrading to MetaPhlAn 4.0).

How to perform a fresh install of HUMAnN 3.6:

How to upgrade from earlier versions of HUMAnN 3:

  • $ pip install humann –upgrade (will upgrade the existing HUMAnN software).
  • You DO NOT need to re-download the latest (v3.1) pangenome database, the DIAMOND-formatted UniRef90/50 databases, or the accessory mapping files to use HUMAnN 3.6. You can point your HUMAnN 3.6 installation to the locations of these existing files using the humann_config script.
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Hello franzosa,
The humann3.6 is not being installed by Anconda installed it still installs the 3.0.1 or 3.0 version. So I installed the HUMAnN3.0 using conda command and then installed HUMAnN3.6 by downlading it from your github account. But now it requires DIAMOND 2.0.15 as you said, and conda is unable to install it due to other dependency issues.

At the end I had to change the config.py file and change requirement of DIAMOND version to 0.9.24 and use it.
Please tell me what i can do? as i would like to use latest version of DIAMOND if possible, Thank you.

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Might be an issue with one of the other packages in the environment causing a conflict. V3.6 is on conda: Files :: Anaconda.org. You could try conda install humann=3.6 and see what happens.

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I solved the issue, I installed the diamond2.0.15 first in environment, then installed the humann3.0, which is the only possible installation by conda in this environment, later i installed the Humann3.6 by downloading the zip file from GitHub and extracting it in bin folder of current environment and installing it using

$python setup.py install --bypass-dependancies-install

. And then installed Metaphlan and Kneaddata. By doing this you can avoid all compatibility issues.

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Were you following the conda install instructions from this link?

https://huttenhower.sph.harvard.edu/humann

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No, those instructions does not work. Because if you install humann by command

conda install humann -c biobakery

It will install too much older version of DIAMOND 0.9.24, so you must first install the latest version of DIAMOND using,

conda install -c bioconda diamond

it will install latest version, and then install the humann 3.0 and later update it using github zip file.