[Taxonomy Output Bug] skingdoms field still outputs 0 in v2.1.13, despite adding support for new NCBI ranks

[dskwei]

I noticed that v2.1.12 release notes state that support for new NCBI ranks like domain, realm, cellular root, and acellular root has been added. However, after rebuilding the database with the latest, unmodified taxdump files, the database build log still shows superkingdom 0. When running a search and requesting the skingdoms field in the tabular output, the result is still 0. Is the issue of mapping the new ranks (e.g., domain for Eukaryota/Bacteria) to the old output field skingdoms still unresolved in v2.1.12/v2.1.13? The current workaround is still to use sed to replace the new ranks with 'superkingdom' before running makedb.

[bbuchfink]

The superkingdom rank has been replaced, so I don't intend to fix the skingdoms field by mapping it to something else. I will include new output fields for the other ranks soon.

[dskwei]

Got it, thanks for the clear explanation!

I understand the plan to phase out 'skingdoms' and introduce new rank fields (like for 'domain' and 'realm') in a future release. That makes sense.

For now, I'll continue with the manual workaround (sed replacement) to populate the rank fields until the new fields are available.

Thanks again for the fast response!

[bbuchfink]

The latest release now has sRANK fields for any rank in the taxonomy.