Intervals in frequency panels


I’m trying to change the interval how frequencies are shown in the frequency panels, but by reading the documentation, I’m not sure what parameter does that. I tried editing pivot_interval and narrow_bandwidth, but nothing changed.

After updating augur, I tried to set --pivot-interval-units = weeks, but that led to this error message:

augur: error: unrecognized arguments: --pivot-interval-units weeks

Any suggestions?

Thank you,

You are on the right track, @andersonbrito! You’ll want to modify the --pivot-interval and/or --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. :slight_smile: )

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Hi @jlhudd,

My latest update led to augur 10.2.0. I updated augur inside conda, following these instructions, using the command below.

# Update Nextstrain dependencies (mafft, etc.), Augur, and Nextstrain CLI.
conda update --all

It seems that is not the latest version, though. I see here that it is now on version 11.3.0.

What would be the best way to update augur?


Anderson Brito


I have now update augur using pip. It gave me augur 11.3.0, I made the edits you suggested above, and the frequency plot now shows weekly intervals.

Thank you for your help.