Error in rule export

[sunshine1126]

Hello, I have an error in augur export as the following:

usage: augur export [-h]
                    Augur export now needs you to define the JSON version you
                    want, e.g. `augur export v2`. ...
augur export: error: argument Augur export now needs you to define the JSON version you want, e.g. `augur export v2`.: invalid choice: 'results/tree.nwk' (choose from 'v2', 'v1')
[Sat Apr  4 22:18:46 2020]
Error in rule export:
    jobid: 1
    output: auspice/zika-colombia_tree.json, auspice/zika-colombia_meta.json
    shell:
        
        augur export             --tree results/tree.nwk             --metadata results/metadata.tsv             --node-data results/branch_lengths.json results/traits.json results/nt_muts.json results/aa_muts.json             --colors config/colors.tsv             --auspice-config config/auspice_config.json             --output-tree auspice/zika-colombia_tree.json             --output-meta auspice/zika-colombia_meta.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: ~/test/zika-colombia/.snakemake/log/2020-04-04T220952.731739.snakemake.log

could you please tell me how to solve this problem? thanks

[huddlej]

@sunshine1126 The zika-columbia repository uses an older version of the augur command line tools than is referenced in the documentation. If you are interested in running an analysis of any Zika sequences (not specifically for this Columbia work), you can follow the Zika tutorial [1] or checkout the full Zika repository for Nextstrain [2].

To run the analysis from the zika-columbia repository, specifically, you can install an older version of the augur tools as follows:

python3 -m pip install nextstrain-augur==5.4.1

This should uninstall the latest version of the augur tools and install a version for which there is only a single augur export option.

[1] https://nextstrain.org/docs/tutorials/zika[2] https://github.com/nextstrain/zika/

[sunshine1126]

Thanks for your reply @huddlej and I just want to use the sample Zika data for learning the usage of the NextStrain.