Hi @SoilRotifer,
I noticed that when using "qiime rescript get-gtdb-data", the species-level info is incomplete. For example, "s__Escherichia coli" only shows as "s__Escherichia", missing everything after the space.This makes genus and species levels look the same, may because of GTDB's taxonomy system. Looks like this might be a bug worth reporting to the maintainers.
Just a heads-up! Thanks!
Hi @GSH ,
Which version of QIIME 2 and RESCRIPt are you using?
Could you please type the following command and share the output?
qiime info
Yeah, here's the output:
System versions
Python version: 3.8.15
QIIME 2 release: 2024.2
QIIME 2 version: 2024.2.0
q2cli version: 2024.2.0
Installed plugins
alignment: 2024.2.0
composition: 2024.2.0
cutadapt: 2024.2.0
dada2: 2024.2.0
deblur: 2024.2.0
demux: 2024.2.0
diversity: 2024.2.0
diversity-lib: 2024.2.0
emperor: 2024.2.0
feature-classifier: 2024.2.0
feature-table: 2024.2.2
fragment-insertion: 2024.2.0
longitudinal: 2024.2.0
metadata: 2024.2.0
phylogeny: 2024.2.0
quality-control: 2024.2.0
quality-filter: 2024.2.0
rescript: 2024.2.2
sample-classifier: 2024.2.0
taxa: 2024.2.0
types: 2024.2.0
vsearch: 2024.2.0
Hi @GSH ,
Thanks for this information. This bug was already discovered in June 2024 and fixed in versions 2024.5.1 and later, as announced here:
Could you please install the latest version and let us know if you still encounter an issue?
My conda version doesn't support installing up to 2024.5, so I installed 2024.2 instead. However, I’ve already resolved the issue by matching the species information from the GTDB database.
Thanks for your efforts!