nextstrain / avian-flu Goto Github PK

Hi, I'm trying to run the quickstart-build for avian-flu, but I got this error. I'm using nextstrain.cli v.6.2.1 and augur v.19.2.0. Some idea to fix it?

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ERROR: Augur version incompatibility detected: the JSON results/branch-lengths_h5n1_ha.json was generated by {'program': 'augur', 'version': '19.2.0'}, which is incompatible with the current augur version (21.1.0). We suggest you rerun the pipeline using the current version of augur.
[Tue Apr 18 21:08:44 2023]

Error in rule export:
jobid: 1
input: results/tree_h5n1_ha.nwk, results/metadata_h5n1_ha.tsv, results/branch-lengths_h5n1_ha.json, results/traits_h5n1_ha.json, results/nt-muts_h5n1_ha.json, results/aa-muts_h5n1_ha.json, results/cleavage-site_h5n1_ha.json, results/cleavage-site-sequences_h5n1_ha.json, config/auspice_config_h5n1.json
output: auspice/flu_avian_h5n1_ha.json
shell:

augur export v2 --tree results/tree_h5n1_ha.nwk --metadata results/metadata_h5n1_ha.tsv --node-data results/branch-lengths_h5n1_ha.json results/traits_h5n1_ha.json results/nt-muts_h5n1_ha.json results/aa-muts_h5n1_ha.json results/cleavage-site_h5n1_ha.json results/cleavage-site-sequences_h5n1_ha.json --auspice-config config/auspice_config_h5n1.json --include-root-sequence --output auspice/flu_avian_h5n1_ha.json

(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-04-18T210843.145552.snakemake.log
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They are many clades for H3N2, who can tell me who defined them?

Hi, in augur align you are calling --fill-gaps which is just doing

 _seq = _seq.replace('-', 'N')

so that in the nextstrain tree everyone gets a FCS.

I don't have access to filtered_H5Nx_HA.fasta and metadata-with-clade_H5Nx_HA.tsv so I can't make a proposal of modification of the Snakemake with a python script in order to leave the FCS indels but if I did I would be happy to make some tries.

The only experiment I did was to download a few thousands of H5Nx sequences from genbank, to label with LPAI those with a deletion at the FCS, then to remove from the alignment the FCS region, to run mega, and I got that the LPAI sequences where quite clustered together.