Problems for the SARS-CoV-2 Workflow

Dear nextstrain team, when we run the SARS-CoV-2 Workflow, why some variants (such as XBB.1.16, BA.2.75) not found in tree and they don’t show up in the
We have uploaded our data under ncov/data/. This is our run command:nextstrain build . --configfile ncov-tutorial/custom-data.yaml

The nextstrain version has updata to the latest version (nextstrain.cli 6.2.1), and the SARS-CoV-2 Workflow version also has updata to the latest version (v12).
Looking forward to your reply!

Hi there,

It’s hard to debug your problem with the limited information you provided (the output of augur export).

What data do you start with? Have you checked that there are some XBB.1.16 and BA.2.75 in there?

In general, to debug this, you can trace the files in the workflow and see where some sequences get lost/filtered out. It’s normal that not every lineage is present in the tree as there are now more than 15m sequences and ~3000 Pango lineages, with around the same order of magnitude of sequences in a standard ncov run.

If you’d like me to have a look:

  1. Please share the entire log file of your run (you can paste it here in the forum or send it to
  2. Ideally, also share your input files