Error with example analysis: configfile can't be set to a list

Hi Nextstrain devs & users,

I’ve cloned the ncov repo with the (amazing) new tutorial and tried running the example analysis with:
snakemake --profile ./my_profiles/example

This is where I run into the error:
snakemake: error: configfile can’t be set to a list ‘[‘defaults/parameters.yaml’, ‘my_profiles/example/builds.yaml’]’ unless its action type is changed to ‘append’ or nargs is set to ‘*’, ‘+’, or > 1

I am working with the following package versions in my nextstrain conda environment:

python 3.6.10
nextstrain-augur 9.0.0
nextstrain-cli 2.0.0.post1
snakemake 5.10.0

Any help in getting past this error would be appreciated :slight_smile:

Hi @nadeaus! To help us dig into this a little more, can you copy and paste the output you get from running the following commands?

conda activate nextstrain
which snakemake
snakemake --version
snakemake --help | grep configfile

The specific Snakemake error you’ve encountered happens with much earlier versions of Snakemake (prior to v5.7.0), so my first thought is that somehow you might have an earlier version installed that is taking precedence of the version you’ve installed in your conda environment. The output of the commands listed above should help us rule out this hypothesis.


Hi @jlhudd thanks for the quick & helpful reply! You were right that the actual snakemake version being used was an old one (5.3.0). I was able to run the example analysis after upgrading snakemake and numpy:

conda activate nextstrain
pip install --upgrade snakemake
pip install --upgrade numpy

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That is great, @nadeaus! I’m glad it’s working. Let us know if you have other questions about the tutorial as you work through it.