Humann 3.0 and bowtie metaphlan output

Greetings i would like to ask, is it possible, from a separate run of metaphlan 3.0 to take the bowtie output and give it to humann 3.0 as an input file?

Thank you in advance for your reply!

If you give HUMAnN bowtie (SAM) output it will treat it as mappings of reads against pangenomes, whereas the MetaPhlAn bowtie output is a mapping to marker genes only. You can provide MetaPhlAn bowtie output to MetaPhlAn to regenerate a species profile and then provide that to HUMAnN via the --taxonomic-profile flag. This will avoid needed to restart a MetaPhlAn run from scratch inside or outside of HUMAnN.

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thank you appreciate it!

as a novice user, I didn’t quite follow that explanation.

For a colleague, I am trying to add a Humann3 analysis as an optional step after Metaphlan3 profiling. The Metaphlan stage produces both a sam.bz2 file and a taxonomic profile (and Graphlan etc all work fine at the moment).

When I pass both to Humann, I get:

Pathway J07447-L1_S37_L001_Abundance

UNMAPPED 0.0000000000
UNINTEGRATED 0.0000000000

So something is not working. If I only try to pass a taxonomic profile, Humann3 complains that it also needs “-i”.

Metaphlan 3 is the latest version, installed in a Docker Container using the latest Chocophlan database from a local directory.
Humann3 is currently installed “as is” in a Conda environment, using the latest version from the Biobakery Channel (since I am testing this before building a new container). No additional databases beyond what comes with the the Conda recipie are installed. So I am not sure if and how Humann3 has access to all the pathway mappings etc - it’s a little unclear from the documentation, to be honest.


What would a simple series of command look like for this to work?

Hi, just a friendly bump - still stuck on this.

HUMAnN will still need a metagenome or metatranscriptome (in e.g. FASTQ format) passed as input. Providing the MetaPhlAn taxonomic profile to HUMAnN is a shortcut: i.e. telling HUMAnN “assume these species are present” rather than working out who’s there yourself. The next step is to map the meta-ome against those species’ pangenomes, hence still needing that file as the primary input (-i).