I have a question about the GTDB Taxonomy and prob...
# magv
Victor de Jager
03/24/2026, 3:31 PMI have a question about the GTDB Taxonomy and probably I am missing a setting.
I only have taxonomy information on a subset of my MetaBAT2 bins. No tax info for the CONCOCT, COMEbin, MaxBin2, MetaBinner or SemiBin2 bins that are created
When I run any of those bins manually with gtdbtk, I get tax info for most of them. Is there a setting I am overlooking? Some of these bins are 1M or bigger.
Also, I don't get taxinfo for some of the MetaBAT2 bins, that do classify in a manual GTDBtk run.
I don't see any errors in the output (.nextflow.log)
A bit unrelated question: is anyone working on adding binchicken? https://aroneys.github.io/binchicken/
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Diego Alvarez Saravia
03/24/2026, 5:17 PMHi @Victor de Jager. Bins are filtered by completeness and contamination before feeding them into GTDB-Tk. Check ``--gtdbtk_min_completeness`` and ``--gtdbtk_max_contamination``, defaults are 50 and 10, respectively.
https://nf-co.re/mag/5.4.1/parameters/#gtdbtk_min_completeness
Diego Alvarez Saravia
03/24/2026, 5:25 PMRegarding binchicken, nobody is working on that. But, isn't binchicken a Snakemake pipeline itself? And it uses Aviary (not sure if it's possible without running Aviary though).
Diego Alvarez Saravia
03/24/2026, 5:27 PMAnd if that’s the case, at least I don’t feel like committing the heresy of running Snakemake inside Nextflow 😅.
😆 1
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James Fellows Yates
03/25/2026, 9:01 AMit's not unheard of 😏 @Edmund...
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Victor de Jager
03/25/2026, 2:46 PMThen, lets not go down that snake alley.
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