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Fix typo in logging message for reference genomes #682

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Merged
pchaumeil merged 5 commits into from
Jan 12, 2026
Merged

Fix typo in logging message for reference genomes #682

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2e9d4c1
Merge pull request #664 from Ecogenomics/staging
aaronmussig Sep 12, 2025
78c962a
Merge pull request #679 from Ecogenomics/staging
pchaumeil Dec 10, 2025
5cdb5f8
Update installation documentation to remove Mash
pchaumeil Dec 10, 2025
4461f70
Merge pull request #681 from Ecogenomics/staging
pchaumeil Dec 12, 2025
0f0ef4a
Fix typo in logging message for reference genomes
lucaspatel Dec 13, 2025
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4 changes: 1 addition & 3 deletions docs/src/installing/index.rst
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Expand Up @@ -104,9 +104,7 @@ GTDB-Tk makes use of the following 3rd party dependencies and assumes they are o
* - `FastTree <http://www.microbesonline.org/fasttree/>`_
- >= 2.1.9
- Price MN, et al. 2010. `FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835736/>`_. *PLoS One*, 5, e9490.
* - `Mash <https://github.com/marbl/Mash>`_
- >= 2.2
- Ondov BD, et al. 2016. `Mash: fast genome and metagenome distance estimation using MinHash <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x>`_. *Genome Biol* 17, 132. doi: doi: 10.1186/s13059-016-0997-x.



Please cite these tools if you use GTDB-Tk in your work.
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2 changes: 1 addition & 1 deletion gtdbtk/external/skani.py
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Expand Up @@ -159,7 +159,7 @@ def run_all_vs_all(self, ql, rl,reverse_ql,reverse_rl,tmpdir,skani_preset=None,s


# lets sketch all genomes first
self.logger.info('Sketching refence genomes')
self.logger.info('Sketching reference genomes')
ref_sketch = self.sketch_references(rl,tmpdir,skani_sketch_dir,skani_preset)
self.logger.info('Done')

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