Breaking Changes to
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!
- Possible error/warning messages:
> > "WARNING: the
--outputflag will be deprecated in the next major augur release. Use
augur: error: unrecognized arguments:
To specify the JSON file to write ancestral mutations/sequences to, use the argument
ancestralnow 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.
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.
augur export. Find out how to adjust your
augur exportcall to work with the latest version using our handy guide.