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

**URL:** <https://forum.biobakery.org/t/humann-3-9-conda-install-will-not-work-please-update-your-version-of-metaphlan/8484>\
**Category:** HUMAnN\
**Created:** [September 8, 2025, 1:36am UTC](https://forum.biobakery.org/t/humann-3-9-conda-install-will-not-work-please-update-your-version-of-metaphlan/8484 "2025-09-08T01:36:49Z")\
**Posts on this page:** 1\
**Showing post:** 4

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**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [February 23, 2026, 11:03pm UTC](https://forum.biobakery.org/t/humann-3-9-conda-install-will-not-work-please-update-your-version-of-metaphlan/8484/4 "2026-02-23T23:03:54Z")

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@franzosa ,

An update to my post.

I realized my MetaPhlAn 4.0.6 is actually older than vJun23 database support, and that is the real problem. So I did the following:

$ conda remove metaphlan

$ conda install metaphlan=4.1

$ conda install humann=3.9

Then, Reinstall the database

$ metaphlan --install --index mpa\_vJun23\_CHOCOPhlAnSGB\_202307 --bowtie2db humann3\_db/metaphlan\_db\_vJun23

I was able to run the metaphlan test using:

$ metaphlan --input\_type fastq examples/demo.fastq.gz --bowtie2db humann3\_db/metaphlan\_db\_vJun23 --index mpa\_vJun23\_CHOCOPhlAnSGB\_202307 -o test.txt

where test.txt starts with #mpa\_vJun23\_CHOCOPhlAnSGB\_202307 as expected

but still can’t run the humann demo test:

humann -i examples/demo.fastq.gz -o examples/SAMPLE2 --threads 16 --protein-database humann3\_db/uniref --nucleotide-database humann3\_db/chocophlan --metaphlan-options “–bowtie2db humann3\_db/metaphlan\_db\_vJun23 -x mpa\_vJun23\_CHOCOPhlAnSGB\_202307”

which tells me:

CRITICAL ERROR: Can not call software version for metaphlan

Would you please help me understand what I am missing?

Thanks!

Faezeh

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