# Usegalaxy.eu HUMAnN 3.9+galaxy1 fails because ChocoPhlAn directory contains mixed database versions

**URL:** <https://help.galaxyproject.org/t/usegalaxy-eu-humann-3-9-galaxy1-fails-because-chocophlan-directory-contains-mixed-database-versions/18339>\
**Category:** usegalaxy.eu support\
**Tags:** troubleshooting\
**Created:** [August 25, 2026, 12:52am UTC](https://help.galaxyproject.org/t/usegalaxy-eu-humann-3-9-galaxy1-fails-because-chocophlan-directory-contains-mixed-database-versions/18339 "2026-08-25T00:52:12Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Hc\_G](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hc_g/32/8935_2.png) [@Hc\_G](https://help.galaxyproject.org/u/Hc_G)\
**Post date:** [August 25, 2026, 12:52am UTC](https://help.galaxyproject.org/t/usegalaxy-eu-humann-3-9-galaxy1-fails-because-chocophlan-directory-contains-mixed-database-versions/18339/1 "2026-08-25T00:52:12Z")

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```auto
Hello Galaxy team,

I am running HUMAnN on usegalaxy.eu and encountered the same
ChocoPhlAn version error reported in this previous topic:

https://help.galaxyproject.org/t/humann-fails-due-to-metaphlan-database-mismatch/16501

Server: usegalaxy.eu
HUMAnN: 3.9+galaxy1
MetaPhlAn: 4.2.4+galaxy0
MetaPhlAn database: mpa_vJun23_CHOCOPhlAnSGB_202403
HUMAnN nucleotide database: chocophlan-full-3.9-29012026
HUMAnN protein database: uniref-uniref90_diamond-3.9-28072025

Error:
CRITICAL ERROR: The directory provided for ChocoPhlAn contains files
(g __Bacteroides.s__ Bacteroides_vulgatus.centroids.v296_201901b.ffn.gz)
that are not of the expected version. Please install the latest version
of the database: v201901_v31

The error was reproduced after rerunning the job.
History ID: 11ac94870d0bb33a0bfc94978ea9ccd1
Job ID: 4838ba20a6d8676535352c7fa7e631d3

Could you please confirm whether the cached ChocoPhlAn directory contains
mixed database versions and which HUMAnN/ChocoPhlAn combination is
currently supported on usegalaxy.eu?

Thank you.

```

---

<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [August 25, 2026, 3:29am UTC](https://help.galaxyproject.org/t/usegalaxy-eu-humann-3-9-galaxy1-fails-because-chocophlan-directory-contains-mixed-database-versions/18339/2 "2026-08-25T03:29:16Z")

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> [@HUMAnN fails due to MetaPhlAn database mismatch](https://help.galaxyproject.org/t/humann-fails-due-to-metaphlan-database-mismatch/16501/2):
>
> Hello @sri_microbiome
> 
> To incorporate HUMAnN with MetaPhlan, please try following the protocol outlined in this tutorial and associated workflows!
> 
> - 🎓 [Hands-on: Metatranscriptomics analysis using microbiome RNA-seq data / Metatranscriptomics analysis using microbiome RNA-seq data / Microbiome](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics/tutorial.html)
> 
> The reads are prepared, then sent through both tool pipelines independently, then the results from each are merged together after. This is what allows the reference data sources to work together.
> 
> Hope this helps! 🙂

Please give this a try! 🚀