[RESOLVED] bug in RESCRIPt get-gtdb-data action in initial 2024.5 release

We recently detected a bug in the RESCRIPt plugin in the initial 2024.5 release, affecting the get-gtdb-data action, which automatically downloads and formats sequences and taxonomy from the Genome Taxonomy Database (GTDB), e.g., for taxonomic classification.

Due to a recent update in how the GTDB taxonomy is parsed, a bug was introduced that caused the taxonomy to complete only from kingdom to genus level. Species-level information was being ignored. The taxonomy was otherwise correct, so this bug would not impact the validity of results, but could be misleading, as no species information would be reported.

Affected versions of RESCRIPt:

Patched version of RESCRIPt:
2024.5.1 (and later)

This bug has been fixed and patched in an updated 2024.5 release. So if you plan to use this action we recommend installing the latest QIIME 2 release, which contains the patched version of RESCRIPt. If you are unsure whether your QIIME 2 environment is affected, run the following command from inside your activated environment:

conda list rescript

If you see a version number ≥ 2024.2.0 and < 2024.5.1, you should install the latest release. If you see a version number ≥ 2024.5.1, or a version > 2024.2, then you have a version of RESCRIPt installed that is not impacted by this bug.

Likewise, if you have generated a GTDB database that you used for taxonomy classification and are unsure if your data are impacted, you can check the provenance information to see which version of RESCRIPt was used to generate those data, following the same criteria as above.

We apologize for any inconvenience this may have caused.

Happy :qiime2:ing


2 off-topic replies have been split into a new topic: installation conflict: QIIME 2 v2024.5 and q2-greengenes2

Please keep replies on-topic in the future.