ERROR::No fixed effects included in formula

I could run MaAsLin2 (Galaxy Version 1.8.0) on the Galaxy server at successfully using the example data (HMP2_metadata.tsv, HMP2_taxonomy.tsv).

I then bring my own data into the same format like these two example files. But the analysis fails. I think this because the Galaxy MaAsLin2 still somehow thinks this is about “dysbiosis” and “diagnosis” (?!)… which I do not have, they were in the example but not in my project… not sure why it fails… I am a beginner! Please advise.

[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
[1] "Creating output figures folder"
2024-02-01 06:38:59.712143 INFO::Writing function arguments to log file
2024-02-01 06:38:59.727243 INFO::Verifying options selected are valid
2024-02-01 06:38:59.728262 INFO::Determining format of input files
2024-02-01 06:38:59.729368 INFO::Input format is data samples as rows and metadata samples as rows
2024-02-01 06:38:59.734782 WARNING::Feature name not found in metadata so not applied to formula as fixed effect: diagnosis , dysbiosis
2024-02-01 06:38:59.735986 ERROR::No fixed effects included in formula.

Hello Anton,

I had exactly the same problem with MaAsLin2, I am waiting for someone that could help us.


Yes it’s weird because the Galaxy server version of maaslin2, there doesn’t seem to be any way of telling the system what fixed and random effects my own project as! There is only a way to load the data and metadata, and run it. But we seemingly cannot enter any parameters?! I am wondering how this is intended to be used. I wish the developers could respond.

Hi sorry everyone,

I apologize for the slow reply here. I am currently working with our galaxy team to figure out what’s going. Rest assured I will get to the bottom of this and update you as I have more information.

Jacob Nearing

Following up on Jacob’s post:
We have a solution for the problem.
I will post when the issue is fixed, hopefully in the next few days
George Weingart PhD
Huttenhower Lab