Open cimendes opened 1 year ago
Hi @cimendes,
This is expected behavior of augur clades
when the node does not have the amino acid and nucleotide mutations that match your clade definitions.
I suspect you need to update the coordinates within clades_h3n2_ha.tsv
.
Currently, it is an exact copy of the H3N2 clades.tsv from the seasonal-flu repo, which was created based on the seasonal-flu repo's reference.fasta and genemap.gff.
If you look at the seasonal-flu's genemap.gff, it has different start/end coordinates than the coordinates listed for your reference in reference_h3n2_ha.gb
.
Also note that the --reference
option is not a supported feature yet. You should have seen this warning when you tried to use this option.
Although it is unexpected that using the --reference
option affected your output, that sounds like a bug that should be fixed!
Just coming back to this issue:
Hi @jrotieno, the issue you are running into is slightly different. Nextclade uses a different algorithm for clade assignment that is separate from the augur clade
command.
As noted in the Clade assignment section:
Nextclade assigns the clade of the nearest reference node found during the Phylogenetic placement step.
Since the two references use different reference trees, they could potentially assign different clades to the same sample.
in which cases should one be used over the other?
Others will definitely have more insight here, but older samples would require an older reference since they are aligned against the reference for mutation calling.
Current Behavior
When running
augur clade
command the JSON file produced only has a partial list of assigned clades, with the remaining showing as "unassigned". When using the--reference
option all branches are set to "unassigned"Expected behavior
All branches should be correctly assigned with the clade information
How to reproduce
I'm using the following docker container:
quay.io/biocontainers/augur:22.0.2--pyhdfd78af_0
With the following command:
augur clades --tree kilifi_H3N2_new_docker_timetree.nwk --mutations kilifi_H3N2_new_docker_nt_muts.json kilifi_H3N2_new_docker_aa_muts.json --clades clades_h3n2_ha.tsv --output-node-data test_clades.json
Here are all the input and output files: augur_clade_input_output.zip
with the
test_clades.json
having the following content:Your environment: if running Nextstrain locally
auspice 2.7.0
):Additional context
Add any other context about the problem here.