Not able to upgrade HumanN to version 3.9

Hi, I’m trying to upgrade the humann from v3.8 to v3.9 using this commend :

pip install humann --upgrade

However, It occurs error. Do you know how to solve this?

P.S I installed HumanN using commend : conda install -c conda-forge -c bioconda humann -y

Follwing is my pip list


I am not sure if it helps, but I rencently installed the version 3.9 recently using:

mamba create -n HUMAnN
mamba activate HUMAnN 

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

mamba install humann -c biobakery

My understanding is that, while you can theoretically use pip to upgrade a conda install, it is not recommended as the two systems manage dependencies differently. It is probably better to do a fresh pip install OR try to upgrade via conda.

@gjordaopiedade Thanks for your advice
I’ve remove my humann and try to install humann with your commend.
Hoever, I can only get humann=3.6


I’ve sucessfully installed humann v3.8 by following the command:
conda install -c conda-forge -c bioconda humann -y

Howver, when i try to upgrade humann with conda command

conda upgrade humann

It still remains version 3.8.

I’ve try adding the biobakary channel into my conda config and conda upgrade humann again.
However, it seems will downgrade humann to version 3.6

It was solved when I restart the terminal.
Can update humann to v3.9 using command

pip install humann --upgrade


Glad you were able to update. We always recommend updating with the pip --upgrade approach since the PyPI package is the first one we update when we release a new version of HUMAnN (sometimes the conda package isn’t immediately available).

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