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Thanks for maintaining this great software! I'm having an issue with easy-taxonomy using GTDB (but not NCBI with the same query input), described below. Using a conda install of version 15.6f452.
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Hello Developer,
I am currently using the database available at http://ftp.tue.mpg.de/ebio/projects/struo2/GTDB_release207/kraken2/ for my analysis with Kraken2, and I've found it quite straightfor…
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Support for the latest release of GTDB would be nice to have.
I've experimented with it. So far the hinder is in `download_gtdb_metadata`. The file name for the metadata file has changed, going from…
lguy updated
4 months ago
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**- [X ] I checked and didn't found a related issue,e.g. while typing the title
**- [X ] ** I got an error in the following rule(s):** ` `**
Error in rule classify
jobid: 109
input: geno…
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I used sequencing data to align with Bowtie2 to the GTDB database, and then I used the gtdb_to_taxdump.py and acc2gtdb_tax.py scripts to generate name, nodes, and acc2tax files. However, I encountered…
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I am trying to run this script but it keeps returning with this
"The genomes.instruction file has been updated with 0 genome(s) taxonomy indications, using '.fasta' extension"
Could you please tel…
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Hi. I attemps to identify the viral entities from a group of the bacterial and archaeal genomes deposited in GTDB.
Identification of viral sequences from GTDB using Genomad exhibited lots of viral …
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Hi,
I'm trying to run genome updater on a mac (macOS Monterey v12.6.3), I've run into some issues which were previously described and ran the troubleshooting steps (e.g. installing xargs and coreut…
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Thanks for writing `taxor` and including useful databases!
What the community (or maybe just me) really wants is a database that covers more of the microbial kingdom, but with the benefit of GTDB f…
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Someone reported anonymously:
### Website URL
https://gtdb.org
### What browser are u using?
Firefox 122
### Version
1.1.4
### Issue type
general
### Notes