Plugin error from composition: An error was encountered while running ANCOM-BC in R (return code 1)

Technical Support
1

Thank you to anyone willing to help.

I followed the steps in the "Moving Pictures Tutorial" for all my analyses, but I encountered an issue during the final differential abundance analysis. Specifically, I’ve been continuously running into problems when using ANCOM-BC, even after looking through all the related posts on the forum and reinstalling my QIIME 2 environment (by the way, it's qiime2-amplicon-2024.5). The error persists.

Below is the error message I received, which I have stored in this log file:
ancombc_error.txt (5.3 KB)

Additionally, here are my script and the corresponding input files:

qiime feature-table filter-samples
--i-table table.qza
--m-metadata-file metadata.txt
--o-filtered-table C24-filtered-table.qza

qiime taxa collapse
--i-table C24-filtered-table.qza
--i-taxonomy taxonomy.qza
--p-level 6
--o-collapsed-table C24-genus.qza

qiime composition ancombc
--i-table C24-genus.qza
--m-metadata-file metadata.txt
--p-formula 'Time'
--o-differentials C24-genus-ancombc.qza

qiime composition da-barplot
--i-data C24-genus-ancombc.qza
--p-significance-threshold 0.001
--p-level-delimiter ';'
--o-visualization C24-genus-barplot.qzv

metadata.txt (211 Bytes)
table.qza (176.0 KB)
taxonomy.qza (182.2 KB)

3

Hi @jjj33,

Thanks for reaching out and providing all of these details! I have a couple of additional questions:

  • When did you install this environment?
  • What operating system are you performing this on (Linux, MacOS, WSL, etc)?
6

Hi @lizgehret
Thanks for helping! Regarding your questions:

  1. Around 1 weeks ago
  2. Linux
7

Hi @jjj33,

Thanks for providing those details!

I've just pushed up a fix to the 2024.5 linux environment files, so if you can do a fresh install of QIIME 2 and re-run ancombc, everything should now work as expected. Thanks for your patience!

9

Dear lizgehret,

following your suggestion, i have deleted the "old" 2024.5 and reinstalled the updated package [I also had an error while running ANCOM-BC in R (return code 1)].

Unfortunately, the installation failed - see below the error message:

$ conda env create -n qiime2a-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml

Channels:

  • released
  • bioconda
  • conda-forge
  • defaults
    Platform: linux-64
    Collecting package metadata (repodata.json): done
    Solving environment: failed
    Channels:
  • released
  • bioconda
  • conda-forge
  • defaults
    Platform: linux-64
    Collecting package metadata (repodata.json): done
    Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

  • nothing provides __glibc >=2.28,<3.0.a0 needed by c-ares-1.33.1-heb4867d_0

Could not solve for environment specs
The following package could not be installed
└─ c-ares 1.33.1** is not installable because it requires
└─ __glibc >=2.28,<3.0.a0 , which is missing on the system.

Please note that the previous installations were all OK - apart from the ANCOM-BC error.

thank for your suggestion/help

Fulvio

10

I have also checked the installed glibc, and the package is present.
Maybe too old?

$ sudo yum install glibc
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile

  • epel: pubmirror1.math.uh.edu
    Package glibc-2.17-326.el7_9.3.x86_64 already installed and latest version
    Nothing to do
12

Hey @fulbag,

Thanks for reaching out - this is definitely strange. The new environment files have been tested successfully, and I also just tried a fresh install on linux and was successful.

What machine are you using (linux, windows via WSL, VM, etc)? And what version of conda do you have installed (you can run conda info if you're unsure)?