ERROR: The MetaPhlAn taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn to at least v3.0

[hammond]

Running this command:

humann –input /g/data/nm31/d/r18_elcho/test/endia50.fastq –output humann-test/ –threads 8

I get this error:

ERROR: The MetaPhlAn taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn to at least v3.0.

I used the conda install and db download instructions online (I can’t post links).

my versions are: humann v3.9, MetaPhlAn version 4.2.2 (4 Jun 2025).

Can you please advise on how to fix this? Thanks.

Please do not flag this as spam again.

[franzosa]

I just wrote up a similar answer here:

Humann 3.9 conda install will not work. Please update your version of MetaPhlAn?

I installed humann3 according to instructions using conda. but there is an incompatability in the versions. Is there any way to actually get humann3 to run? If not can you please point me to instructions for installation / running that work. I used the ones here: " huttenhower.sph.harvard.edu/humann". then had to fix the ‘unknown command –bowtie2out’ , but I am now getting an error that the database versions do not match. I have not changed or specified anything.. I downloaded the databases and…

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