not found


I’m trying to run the example data set example_multiple_inputs but am getting the following augur-related error message (augur is installed and in the path) during the sanitize_sequences step:

Traceback (most recent call last):
File “scripts/”, line 2, in
from import open_file, read_sequences, write_sequences
ModuleNotFoundError: No module named ‘augur’

Any help is greatly appreciated!

Hi @suskraem,

Can you check that you’re using the right Python where augur is installed? Try which python3.

Having a different Python environment activated than the one Augur is installed in is a common cause for errors like you report.

How did you install augur?



Thanks Cornelius,
I figure it out. I was running nextstrain on a compute cluster and the issues was with the sequence of loading modules and environments.

Hi @suskraem, when running the ncov workflow in a cluster environment, you can run Snakemake with --use-conda --conda-frontend mamba. This will tell Snakemake to create the proper Nextstrain conda environment and activate it before running each job. This approach works best on a cluster where you can install Conda yourself (e.g., in your home directory) and saves you the extra work of creating a custom Snakemake job script or asking the cluster IT staff to install and maintain Nextstrain software.

You can read more about this approach in this earlier post about reproducible workflows with conda environments.