ERROR: Augur version incompatibility detected about avian-flu HOT 3 CLOSED

That error indicates that intermediate files from a previous run [1] exist, however you are rerunning the pipeline with a newer version of Augur. The easiest solution is to remove the intermediate files (e.g. remove the results directory, or rename it if you want to keep a backup) and rerun the pipeline; this will force the pipeline to rerun every step with your current augur version.

I'm using ... augur v.19.2.0

The error indicates that you are now using "augur version (21.1.0)", but that a previous run of the workflow used 19.2.0. Note that if you are running the pipeline using a nextstrain-cli provided runtime (e.g. Docker, managed conda) then the version of augur used by the pipeline may be different to augur --version. If you let us know what command you are running the pipeline, as well as the output of nextstrain check-setup, we can help troubleshoot this.

[1] Specifically, results/branch-lengths_h5n1_ha.json was generated by Augur version 19.2.0

from avian-flu.

The commands that I used in the running were:
https://github.com/nextstrain/avian-flu/tree/master/quickstart-build

git clone https://github.com/nextstrain/avian-flu.git
cd avian-flu
nextstrain build quickstart-build/ --dry-run
nextstrain build quickstart-build/
After that I get the error.

As you say I think is a problem with the different version of augur between the running and the avian-flu example. After change the version of augur inside the files the error disappear. The results/branch-lengths_h5n1_ha.json file was created with Augur version 19.2.0 and it cames with the data, so I can't create a new one.

from avian-flu.

The results/branch-lengths_h5n1_ha.json file was created with Augur version 19.2.0 and it cames with the data, so I can't create a new one.

Ah, it probably shouldn't come with the repo. And indeed, it looks like @lmoncla already removed it (and related files in results/).

from avian-flu.