I am encountering the following error:
augur traits is using TreeTime version 0.8.0 Assigned discrete traits to 4631 out of 4631 taxa. NOTE: previous versions (<0.7.0) of this command made a 'short-branch length assumption. TreeTime now optimizes the overall rate numerically and thus allows for long branches along which multiple changes accumulated. This is expected to affect estimates of the overall rate while leaving the relative rates mostly unchanged. ERROR: 300 or more distinct discrete states found. TreeTime is currently not set up to handle that many states. [Wed Feb 10 19:49:39 2021] Error in rule traits: jobid: 14 output: results/NorthAmerica/traits.json log: logs/traits_NorthAmerica.txt (check log file(s) for error message) shell: augur traits --tree results/NorthAmerica/tree.nwk --metadata results/NorthAmerica/metadata_adjusted.tsv --output results/NorthAmerica/traits. json --columns country_exposure division_exposure --confidence --sampling-bias-correction 3 2>&1 | tee logs/traits_NorthAmerica.txt
This is new error for me, I was trying to re-run the NorthAmerican build from a week or so ago. Can someone comment on what I am doing wrong here?
Here is my build:
builds: NorthAmerica: subsampling_scheme: NA auspice_config: "my_profiles/NorthAmerica/auspice.json" region: global subsampling: NA: global: group_by: "country year month" seq_per_group: 1000 ## You could also specify a title which will be used for all builds ## where you haven't already specified a title above: ## (Uncomment this to use!): title: "SARS-CoV-2 Build Focused on North America" files: description: my_profiles/NorthAmerica/description.md exposure: NorthAmerica: trait: "division" exposure: "division_exposure" ######### ## Finally, you can specify what traits you want to reconstruct, per build. ## If you have exposure information for a trait, specify it as well, so that ## this is incorporated into the final run. (Otherwise, it will simply be excluded) ## First, specify the traits you want to reconstruct, per build: ## (uncomment to use!) traits: NorthAmerica: sampling_bias_correction: 3 columns: ["country_exposure"]
I have pre-filtered the metadata to only those samples I want to include from the public NA build, which is why I used 1000 as my filter number here.