[installation failure]

Microbial community profiling MetaPhlAn
1

I need help. I have already created a separate environment and installed python 3.7. However, this problem keeps occurring.

(mpa) C:\Users\me>conda install -c conda-forge -c bioconda metaphlan
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package → Available version

I don’t even know which of the the packages are causing the error.

2

Hi @sasakitomiyano
It seems you have a package incompatibility issue with your conda installation.
When this problem happens, creating the environment already specifying all the packages necessary can help. E.g.
conda create -n metaphlan4 -c conda-forge -c bioconda python=3.7 metaphlan

3

Hello!

I appreciate the help but I’ve still encountered problems even though I’ve taken your suggestion into account.

(base) me@LAPTOP-NGD:~$ conda create -n metaphlan4 -c conda-forge -c bioconda python=3.7 metaphlan
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: - Killed

I’ve been using ubuntu (installed using WSL) if it helps.

Thank you.

4

Hi @sasakitomiyano
It seems during the resolving of the installation, your conda is taking so long resolving the environment that a timeout kills the installation. I am not sure why this is happening, I can only suggest you to reinstall conda from scratch and try on a clean installation

5

Heya @sasakitomiyano,

mamba is a drop-in replacement for conda that is virtually always much faster and more likely to succeed at things installs

I’d try this in the base conda environment:

conda install -n base -c conda-forge mamba

then the environment creation with mamba like so:

mamba create -y -n metaphlan -c conda-forge -c bioconda -c defaults python=3.7 metaphlan

This works for me in less than a minute on both mac and ubuntu that i just tested

then you’d still activate and deactivate with conda

conda activate metaphlan

conda deactivate

hopefully that helps, i put mamba on immediately on any system i use conda :+1: