How to get the latest Lineage- with CLI about nextclade HOT 4 CLOSED

Hi @kiranpatil222, note that the information on clades and lineages comes from datasets. Make sure you are using the latest dataset.

In order for me to be able to help:

• Which dataset are you using? (Nextclade currently provides 5 SARS-CoV-2 datasets; see README.md for each dataset for their purpose)
• Have you downloaded the latest version of the dataset? (You can find the version of the downloaded dataset in pathogen.json file, in version field. You can see release history of all datasets here or in Nextclade Web, or in the CHANGELOG.md file of the downloaded dataset)
• Which version of Nextclade CLI are you using? (type nextclade --version. The release history is here)
• How do you use Nextclade CLI? Provide full commands.
• Which variants and lineages are you missing?

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Hi Ivan, Thank you for the clarification dataset was old, so it was not updating Lineages,
I presumed conda update nextclade will update with dataset.
Just one more question how do we keep track of latest dataset updates.?
or How often it changes

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@kiranpatil222 Datasets are small (a few megabytes at most), so we recommend (in the documentation) that most users download their datasets fresh every time they start a new session, e.g. when you come to the lab in the morning and want to analyze a batch of new data, then re-download the dataset. Or if you are running nextclade as a part of daily automated workflow, then download the dataset in your workflow just before starting nextclade run, i.e. there is no reason to persist the dataset.

If you don't need dataset files on your computer, you can also try nextclade run command with --dataset-name argument instead of --input-dataset. In this case Nextclade will download a fresh dataset in-memory and will run the analysis immediately with it, so that the separate nextclade dataset get command is not needed.

You can track new dataset releases on GitHub Releases page of our data repository:
https://github.com/nextstrain/nextclade_data/releases
You can subscribe to notifications on GitHub by selecting "Watch" -> "Custom" -> "Releases" on the top panel of that page. You can configure GitHub to only send notification within the app (https://github.com/notifications) or to also send emails.

Finally, you can use nextclade dataset list command (optionally with --json flag) to keep track of the list of versions for each dataset, and react when the list changes.

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I will close the issue for now. Please comment or create a new one if there's still outstanding problems.

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