Issue installing Humann3 via conda


I hope this message finds you well. I am encountering an issue while trying to install Humann3 through conda (miniconda3), specifically… stalling at the “solving environment” step.

Here are the details of the issue I am experiencing:

When I execute:
conda install humann -c biobakery

The installation process gets stuck at the “solving environment” step and does not proceed further. I have allowed it to run for an extended period, but it does not show any progress.

Steps I have taken so far to troubleshoot the issue:

  1. Updated Conda: I have updated Conda to the latest version using the “conda update conda” command.

  2. Cleared Conda cache: I have cleared the Conda package cache using the “conda clean -a” command.

  3. Attempted alternative channels: I have tried specifying different channels using the “-c” option, such as “conda-forge” and “biobakery”.

  4. Created a new environment: I have created a fresh environment using the “conda create -n biobakery3” command and attempted the installation within this new environment. However, the issue persists.

  5. I have confirmed the below commands regarding channels were run:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery

Any assistance that can be provided would be much appreciated! Not sure why I am getting stuck!

Thanks alot!

Hello @Jwright , Sorry to hear you are getting stuck and thank you for the detailed post. Do you have anything else installed in the conda environment that you are trying to add HUMAnN too? If so, try creating a new environment and adding HUMAnN first to see if this resolves the issue. My best guess is that there are a few packages already installed and conda is having a very difficult time trying to resolve a lot of different dependencies. If this does not help, double check your python version and maybe try setting it to python 3.7 to see if that helps.


use mamba to install:

conda create -n biobakery4 python=3.7
conda activate biobakery4
mamba install -c conda-forge -c bioconda humann
1 Like

I used mamba as suggested by xiaoafei. Much faster that conda.

Thanks for this tip - I have heard good things about mamba as an alternative for installing conda packages. Apparently it is much faster at solving the dependency graph problems?