Issues installing moshpit 2025.1

Technical Support
1

A similar issue as in Qiime2 with the new conda version (tiopic Trouble installing QIIME 2 2026.1 - #11 by lizgehret) happened with Moshpit

The same happened when I wanted to install Moshpit 2025.10 (and 2026.1)

I do have an extra hurdle: I installed miniconda system wide in /opt/miniconda3 following to also give my fellow users access. It gave some troubles to get there, but it works fine with Qiime2 2025.10 and Sina. I kept a log but do not have time and guts to delete and reinstall the whole conda and its environments.

conda env create \
  --name qiime2-moshpit-2026.1 \
  --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.1/moshpit/released/qiime2-moshpit-ubuntu-latest-conda.yml

output: error:

2 channel Terms of Service accepted
Retrieving notices: done
Channels:
 - conda-forge
 - bioconda
 - https://packages.qiime2.org/qiime2/2026.1/moshpit/released
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages:

Preparing transaction: done                                                     
Verifying transaction: done                                                     
Executing transaction: done                                                     
ERROR conda.core.link:_execute(1033): An error occurred while installing package 'conda-forge::openmpi-4.1.6-hc5af2df_101'.
Rolling back transaction: done                                                  
                                                                                
LinkError: post-link script failed for package conda-forge::openmpi-4.1.6-hc5af2df_101
location of failed script: /opt/miniconda3/envs/qiime2-moshpit-2026.1/bin/.openmpi-post-link.sh

conda clean --all gave a lot of packages that could not be removed due to permissions and sudo conda clean --all did not work at all, output:

WARNING: cannot remove, file permissions: /opt/miniconda3/pkgs/cache

but it seems to remove the packages and

conda install conda=25.11

gave:

2 channel Terms of Service accepted
Retrieving notices: done

DirectoryNotACondaEnvironmentError: The target directory exists, but it is not a conda environment.
Use 'conda create' to convert the directory to a conda environment.
  target directory: /opt/miniconda3/envs

And… conda --version

gave:

conda 26.1.1

So I am stuck.

*Edit: Moshpit version mistake corrected

Trouble installing QIIME 2 2026.1
2

Hi again,

I found a solution, being lucky that I had installed conda before the update to 26.1.1.

I checked revisions with: conda list --revisions. The update to conda version 26.1 happened in the 4th revision, so I ran conda install --revision 3 and tried again to install moshpit (both versions 2025.11 and 2026.1 to get rid of the DirectoryNotACondaEnvironmentError):

==> WARNING: A newer version of conda exists. <==
    current version: 25.11.1
    latest version: 26.1.1

Please update conda by running

    $ conda update -n base -c defaults conda

So, this is an alternative way to revert to conda version 25.11.

I will not upgrade to 26.1 until the openmpi issue has been solved. In the meantime I recommend qiime2 and moshpit users to install conda with conda install conda=25.11.

1 Like
3

Hi Jack,

Thank you for reporting an issue here and for sharing your investigation and solution! :clap:

4

With pleasure Timur,

I still had some issues: Moshpit 2025.10 installed fine, although the BUSCO advise during installation (quast-download-busco) refers to Busco v3/odb9 databases that are not online anymore.

ERROR! Failed downloading bacteria database (url: https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 404: Not Found
You can try to download the file manually, place it in /opt/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/quast_libs/busco/bacteria.tar.gz and restart QUAST
WARNING: Failed to download bacteria database from https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gz and unpack it into /opt/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/quast_libs/busco

same messages for the “eukaryota” and “fungi” databases.

The current versions are v4/odb10 in Index of /v4/data/lineages/

Moshpit 2026.1 install however failed with the following message:

ERROR conda.core.link:_execute(1031): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1'.
Rolling back transaction: done

For now I can continue with version 2025.10 and I will try to get the Busco v3 databases. I would be happy if someone could provide me with a link.

5

I think this one can be fixed with

conda clean --all

But you can't run it, correct?

2 hours ago, one person shared ODB9 databases. Will they work? Check the last post from here: Issues about 'quast-download-busco' · Issue #257 · ablab/quast · GitHub.

6

Yes that worked!

And the databases also exist. [– 3 hrs ago, what a coincidence :slight_smile: ] so everything should work now!

Thanks Timur!

1 Like