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Hi everyone,
Does anyone know solutions for the following error during running gtdbtk de_novo_wf? I think I am getting same error to case [#433](https://github.com/Ecogenomics/GTDBTk/issues/433) th…
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Need to change Escherichia hermannii to the new genus name Atlantibacter. Already done in `development.tsv`. Need to do it in the taxonomy files too.
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I'm building a database that I use with MetaEuk and I have taxonomy information but I'm not sure the correct formatting to use. Also, can there be missing fields to use the taxonomy feature? I have f…
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Hi,
Thanks for a useful tool - I find myself wanting to cite pytaxonkit - what do you suggest? I'm also citing taxonkit itself, just curious aout the bindings.
ta
wwood updated
5 months ago
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Just installing medi. It requires curl package in R for fread function for nextflow run database.nf command. You may want to add r-curl to the .yaml file.
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some taxid that have taxonomy on NCBI but taxonkit not found or not complete
taxonkit v0.15.1
taxonkit lineage 0.txt|less :
20:24:21.750 [WARN] taxid 3046382 not found
20:24:21.751 [WARN] taxid …
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I'm using v0.15.1. It appears the generated nodes.dmp is missing rank information for genomes with repeated GTDB taxon names at different ranks, e.g.:
GCA_009780445.1 d__Bacteria;p__Bacillota_A;c__…
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Hello, awesome update, loving the speed!
Not really an issue per se, but I have a hmmscan database that I would like to use preferentially for taxonomy calls. It's not a comprehensive database, so …
pck00 updated
4 months ago
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### Prerequisites
- [x] make sure you're are using the latest version by `taxonkit version`
- [x] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/)
### Describe your issue
I am tryi…