You are on the right track, @andersonbrito! You’ll want to modify the
--pivot-interval-units arguments for
augur frequencies to change the spacing of frequency estimates. One way to get started would be to copy the existing tip frequencies rule from the main Nextstrain ncov workflow.
If you are already using this rule in your workflow, you can override the default frequencies parameters by defining your own values in your
builds.yaml config file.
Since Augur does not recognize the
--pivot-interval-units argument, my best guess is that the version of Augur is still too old somehow even after you updated. When you run
augur --version, what version do you get?
Also, are you managing your Augur installation through a Conda environment outside of Snakemake or with Snakemake’s
--use-conda flag? Or do you manage Augur with pip? (There are honestly too many ways to install Augur right now. )