I have been trying to run MaAsLin2 on usegalaxy.eu, but the job consistently fails after some time. The error log shows the following messages:
Error: glmmTMB models require glmmTMB >= 1.1.8
Installed TMB version is incompatible
This seems to be a dependency issue on the server side rather than a problem with my input files. I tested with both simple metadata and feature tables, but the error is the same.
Could you please check and update the MaAsLin2 tool environment (especially glmmTMB and TMB versions)?
Thanks for all the details and testing! I’ll check to see if I can reproduce. More soon.
Meanwhile, I’m wondering what happens if you try to toggle into a prior version of the tool? Does that work? I’ll test too but it might get you a very quick working solution if we need to address the dependency package on the current version.
And, since you didn’t mention the version you were using, sometimes workflows have older tool versions that have configurations that are no longer supported (various technical reasons), so you could check and update if needed.
Most current version → MaAsLin 2 Microbiome Multivariable Association with Linear Models(Galaxy Version 1.18.0+galaxy0
Then there are two older versions at the EU server to try out
The first, fourth, and fourth-hybrid test here should all trigger the use of the glmmTMB package as far as I know.
So, maybe the problem is data based, and what you are getting is just a warning from the underlying tool? Those can sometimes confuse troubleshooting and can be ignored in certain cases. Why? Because Galaxy is handling the dependencies in a different way than when the tool is used directly, and this is a warning anyway, not directly leading to “an error”. I think that is what is going on with this tool, since I see the warning even in successful jobs with expected results.
Warning message:
In checkDepPackageVersion(dep_pkg = “TMB”) :
Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.14
Current TMB version is 1.9.15
Please re-install glmmTMB from source or restore original ‘TMB’ package (see ‘?reinstalling’ for more information)
Warning message:
The size argument of element_line() is deprecated as of ggplot2 3.4.0. Please use the linewidth argument instead.
Is there anything else in your logs to troubleshoot from? If you compare to the tool tests (or tutorial data/methods?), can you notice anything else? I see a few topics at the Biobakery forum for this tool/package combination, and the first two are scientific questions, maybe also review for ideas?
Please use the