The bioBakery help forum

Humann3 release date/ Humann2 metaphlan incompatibility

I am using humann2 for a final project which will end mid-june. I’m sending this mail regarding the humann2 incompatibility with metaphlan2.

I’ve been using the conda installation: https://anaconda.org/bioconda/humann2.

Humann2 gets stuck in a loop at when downloading the .mpa file from methaphlan2.
Is this a problem with metaphlan2 or is it a problem with the conda installation?
I’ve also used a docker container for humann3 alpha at: https://hub.docker.com/r/biobakery/humann.

This seemed to work for metaphlan3 but not for diamond (incompatibility issues). This is due to
diamond changing their format. Updating the database results in humann saying there is an incompatible diamond database version. Finally, is there a date when humann3 will be released on conda?

The same HUMAnN 3.0 alpha in the docker is available on our biobakery conda channel. You can get it via conda install humann -c biobakery. We are currently experiencing some instability with the HUMAnN 3.0 database downloads. I intend to make a proper “HUMAnN 3.0 release notes” post here as soon as those are sorted out.

HUMAnN 2.0 and its databases are locked to the DIAMOND v0.8 format whereas HUMAnN 3.0 and its databases use the newer DIAMOND v0.9 format. Hence the databases are not exchangeable. More generally I do not recommend mixing 2.0 and 3.0 components since they are based on separate species lists, marker genes, UniRef releases, etc.