What is the output from the ncov tutorial (https://github.com/nextstrain/ncov) “getting started” build supposed to look like? When I run the build defined in
my_profiles/getting_started/builds.yaml, it runs with no errors and few warnings (see log files in github repository below), but when I view the resulting
auspice/ncov_global.json file in https://auspice.us/, I don’t see any clade frequencies.
my_profiles/getting_started/config.yaml file uses the
defaults/parameters.yaml file, which specifies the
auspice_config file as
defaults/auspice_config.json, which includes “frequencies” in the auspice panels.
In auspice, the left-hand panel says “(Frequencies cannot be normalized)”. I’ve tried running several other builds (with
config.yaml files based on “getting_started” and “example” profiles and using data from either example data or data downloaded from GISAID), but none of the builds I’ve run show frequencies in auspice. In all of the builds I’ve tried running so far, Nextstrain does output a file to
auspice/ncov_global_tip-frequencies.json. In some of the builds, like the one below, the data contained in the tip-frequencies.json file appear to make sense (see
tip-frequencies.png in the repository below. I created the figure in python using the data in
Am I doing something wrong? How do I get frequencies to show in auspice?
Link to github repository: https://github.com/philipshirk/ncov_tutorial_example
git clone https://github.com/nextstrain/ncov.git ncov_tutorial_example cd ncov_tutorial_example/ conda activate nextstrain nextstrain build . --cores 4 --use-conda --configfile ./my_profiles/getting_started/builds.yaml –forceall