HUMAnN Database Error on Galaxy

Microbial community profiling HUMAnN
1

Hello,

I’m encountering an error when trying to use the HUMAnN module hosted on Galaxy EU. I’ve contacted Galaxy support for any aid on their end, and apologies if this forum is only for discussing these tools in local environments.

On Galaxy, the tool-generated error message is as follows:

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 major things I’m trying to figure out first are if …
a) the error stems from my data, specifically the .fastq.gz files I’m specifying as the input
b) the error stems from the version(s) of HUMAnN that Galaxy EU has access to, or the ChocoPhlAn database(s) Galaxy EU has installed

Here’s some context for my files/tools:

  • Shotgun metagenomics reads uploaded to Galaxy via FTP as .fastq.gz files
  • Galaxy HUMAnN version 3.8+galaxy0
  • Over a year ago, I supplied these same .fastq.gz files to Galaxy EU using the FTP file upload, and successfully completed a MetaPhlAn2 analysis using them. I’ve also re-uploaded the MetaPhlan Community Profile files to use with HUMAnN
  • I tried prior versions on Galaxy to try to change this cached database, and could find (for example) “mpa_v30_CHOCOPhlAn_201901” on version 3.6.0+galaxy0, which seems to resemble the version mentioned in the tool-generated error message. However, running my file through this version produced an identical error.

I’ve seen discussions of similar errors in this forum, but for users using HUMAnN in a local environment. In those discussions, it appears the error occurred when database files from previous HUMAnN versions were stored in the same directory as databases from newer HUMAnN versions.

Thank you very much for any advice you can offer. I apologize for the lack of technical depth I can provide on this issue, and please let me know what other info is needed to diagnose the problem.

2

We do not run the Galaxy you are referring to, so we can’t directly fix this. It sounds like they have some files downloaded to the HUMAnN database folder that shouldn’t be there. This is discussed in other posts on this forum if you want to forward those to the Galaxy team to help with the fix?

3

Thank you for the fast response, and I apologize for my delay. I’m in a dialogue with the Galaxy team now so I’ll definitely forward the other discussions to them.