Conda environment error

Hello, I am new to Nextstrain and I have been able to work through the Zika Tutorial without issue. I am currently trying to run an example with the SARS-CoV-2 datasets using the tutorial. I am having trouble with the conda environment. Here is the output from my terminal:

I didn’t see any other threads about this issue, but any help resolving the conda environment issue would be greatly appreciated. Thank you!

Hi @mavoeg,

From your “Checking setup…” output, it looks you are using the Nextstrain Conda runtime. If you run nextstrain setup --set-default conda then all your subsequent nextstrain build commands will automatically run within the Nextstrain managed conda environment.You do not need to manually activate the conda environment.

Thank you for flagging this issue! It looks like our SARS-CoV-2 tutorial needs to be updated to reflect the new Nextstrain Conda runtime.


Hello @joverlee ,

Thank you for taking a look to help me with running the SARS-CoV-2 tutorial. I have run the command you suggested and receiving the same message.

Do you have any other suggestions I might be able to try?

Thank you,


Hi @mavoeg,

You do not need to run conda activate nextstrain. You can skip this step in the tutorial and run the next steps in the tutorial.

We will be removing this step from the tutorial so it does not confuse other users.


To add to @joverlee’s answer: I think the confusion may be that what we call conda is different from the way people usually use conda. It is not a normal user installed conda environment. Instead, what nextstrain CLI does is it sets up a new, hidden conda environment that’s totally separate from a potential user installed conda installation.

When you run conda info --envs you are using the conda that you installed yourself. This is totally separate from the conda nextstrain CLI installed.

When you run a snakemake nextstrain workflow using nextstrain build --conda what happens is that the nextstrain CLI magically uses the hidden/separate conda environment.

The advantage of this setup is that you as a user do not need to worry at all about the nextstrain managed conda environment. It’s abstracted away. It’s installed with a single command, and kept up to date with a single command: nextstrain update conda.

Nothing you do to your conda environment will break that nextstrain environment etc.

You don’t need to activate anything to make nextstrain build --conda work, since nextstrain build automatically “activates” things internally without it being visible to you (or changing any of your settings).

I hope this helps reduce confusion.

Jover, thank you for your assistance!

Yes, this makes sense. I appreciate the clarification.

Thank you!