HUMAnN/MetaPhlAn error

usegalaxy.eu support
,
1

Error while trying to run HUMAnN to annonate reads:

ERROR: The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJun23 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJun23.

HUMAnN calls for the current version of MetaPhlAn which is v4 but the only cached database for classifying community members is from 2022. Can this be updated to at least vJun23 as the error calls for? Thanks!

2

Welcome @Maria_Fernandes-Mar

Is the job failing (red) or is this just a warning in the logs?

I see “June” databases for the tools at the EU server but might be looking at the wrong thing.

Do you want to share your example? The tool versions and databases, exactly, will be needed for me to make a request. You are welcome to generate a shared history link and post that back, and I’ll review. How to share is in the banner topic.

And, as a reference, there might be a better way to do this. See this step in our tutorial for an example, and the rationale → Hands-on: Metatranscriptomics analysis using microbiome RNA-seq data / Metatranscriptomics analysis using microbiome RNA-seq data / Microbiome

Let’s start there, thanks! :slight_smile:

3

Thanks, I misunderstood the error. Apparently, the error meant it can’t generate the taxonomy on HUMAnN using the database available to be cached. And on the tutorial you shared, that is provided as an output of MetaPhlan. But that is also a problem I’m having, MetaPhlan doesn’t run well with classifying my metagenome reads (it only classifies one species), even though I have classified them without a problem using Kraken2..

Captura de tela 2025-07-15 143730
Captura de tela 2025-07-15 143730911×292 16.8 KB

4

Hi @Maria_Fernandes-Mar

Thanks for explaining!

Since MetaPhlan wasn’t classifying your reads well anyway (the newest version, when used directly?) you could try using the Kraken2 output instead in HUMAnN with this converter tool.

  • Krakentools: Convert kraken report file to MetaPhlAn-style

To be clear: it looks to me like the updated indexes are included in MetaPhlAn at UseGalaxy.eu (last updated March 2025). This result can be passed through to HUMAnN. The current usability problems are:

  1. the indexes at EU need to be added a specific shared index resource to make them available at other UseGalaxy servers → Add updated Metaphlan index(es) to CVMFS · Issue #52 · galaxyproject/idc · GitHub (original asked at Metaphlan vJun23)
  2. the file labeling is inconsistent between servers, leading to workflow/shared data table issues for administrators, and confusion for scientists → Make Metaphlan/Humann DBs transferable · Issue #5681 · galaxyproject/tools-iuc · GitHub
  3. those same indexes could be added to the HUMAnN tool as well (what you originally asked about) but the other two items are delaying the consolidation. These databases are large enough to prevent an easy fix (replicate them with multiple names) and multiple labels leads to reproducibility issues we want to avoid. The available path for now is to run MetaPhlAn directly instead a the server that hosts the current index, and to pass the result to HUMAnN for the additional classification layers.

So, there are a few technical issues remaining to be resolved to make this all nicer (for scientists and admins!), but the scientific path with the most current data should be fine. Adding all the tools to a simple workflow would produce about the same total “processing time” per sample. If you need to move data between servers, this can all be done via URL (no download step).

Apologies for the complicated usage! But, does this help? We can follow up more. :slight_smile: