Pipeline components for real-time phylodynamic analysis
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Breaking Changes to augur

This is a list of known 'breaking changes' to augur. These are changes that require users to modify existing scripts or calls to augur functions because the old usage is no longer supported. 'Deprecated' changes, which work for the moment but will no longer be supported in future, are also included.

Note this list only includes changes to augur code and may not cover breaking changes introduced due to changes in dependancy packages. We try to support these too, so please open an issue if you think you've found something we didn't catch.

This list will only be helpful if you are sure the command used to work and only stopped working after you upgraded your augur installation. If your augur installation is from earlier than 2019, or if this list doesn't solve your problem, run --help for the command you're using and use that information to try re-writing your call.

Click on the augur function that used to work, and we'll try to get you up and running ASAP!

ancestral

--output argument

  • Possible error/warning messages:
    > > "WARNING: the --output flag will be deprecated in the next major augur release. Use --output-node-data instead."

augur: error: unrecognized arguments: --output

  • Solution:
    To specify the JSON file to write ancestral mutations/sequences to, use the argument --output-node-data instead of --output.

  • Explanation:
    ancestral now supports outputting a FASTA file of reconstructed ancestral sequences (for FASTA-input runs - this was already supported in VCF-format for VCF-input runs). Users can ask for this output and specify a file name using --output-sequences. Since there are now two types of output from ancestral, the arguments have become more descriptive.

export

Version error

  • Possible error/warning messages:

    augur export: error: the following arguments are required: Augur export now needs you to define the JSON version you want, e.g. augur export v2.

  • Solution:
    We've upgraded augur export. Find out how to adjust your augur export call to work with the latest version using our handy guide.