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@theosanderson raised a good point:
> Hmm does this mean we could be failing to ingest some other quite important data? (Not a criticism - just for understanding, I guess I previously thought we we…
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As per link below, NCBI have changed the 'country' qualifier to 'geo_loc_name', which mean the `ncbi_byid()` function no longer parses the XML and produces a 'country' field.
[https://ncbiinsights.…
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I encountered an issue while running the BACANNOT pipeline, specifically with the GET_NCBI_GENOME process. Here is the error message I received:
```console
ERROR ~ Error executing process > 'BACA…
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tbl2asn has been replaced with table2asn. tbl2asn is no longer available for download as of 18 June 2024.
https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/README
The new r…
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The sequence TRM345 (NCBI GenBank: PP852943) in the current Mpox build is highly divergent, with low coverage and quality. Suggesting its removal from the mpox build. Might also be worth considering a…
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I keep getting the following when attempting to download all the gff and cds-fasta files for Pantoea from NCBI:
"ERROR: Download from NCBI failed: ConnectionError(MaxRetryError('HTTPSConnectionPool…
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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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`cazy_webscraper` is not identifying the NCBI protein version accessions correctly, and is unable to pair up the downloaded data with data in the local CAZyme database.
```bash
Traceback (most rec…
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Is there a way to incorporate genomes into the pipeline that aren’t from genbank/refseq ?
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According to FASTA spec, the start of the header up to the first white space is the sequence id, everything after is description.
The backend currently seems to not follow the specs. Example, note …