ID not found in NCBI lineage #13
Description
Hi,
I just installed taxconverter to convert Kraken2 output to use with Vamb. I'm using the data/clades.tsv file provided in the github, but I'm getting a number of taxids produced by Kraken2 that aren't there:
2025-11-27 02:49:43.215 | INFO | taxconverter.main:get_lineage:67 - ID not found in NCBI lineage: 2100
2025-11-27 02:49:43.215 | INFO | taxconverter.main:get_lineage:67 - ID not found in NCBI lineage: 872331
2025-12-01 13:14:57.802 | INFO | taxconverter.main:get_lineage:67 - ID not found in NCBI lineage: 1118964
.... among others
This is causing VAMB to fail since the taxonomy file is incomplete. Is this likely due to a version incompatibility (my Kraken database was installed over a year ago)? Is there a way to update the clades.tsv file (or generate a new one) based on my Kraken db?
Any help fixing this would be appreciated.
Cheers,
David