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when trying to add NCBI taxonomy information while running in nucleotide mode (`-z`), it doesn't seem to be pulling the taxid info, as these messages are popping up and there is no tax added in the ou…
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I will try to get the nuccore accessions, taxid where available
low priority request, but would be good for identifying Diphtheria
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### Description of the bug
Mismatches in naming of the Refseq post-alignment and pathogen annotation sheet lead to some organisms not being report. Consider 2 options:
1. More intensive - adding ta…
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Hi there,
I am seeing very low mapping rates (~10-15%) for my whole genome sequencing data using Kraken 2. Samples are gut microbiome samples from patients with heart disease, sequenced on Illumina…
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## Short description of the problem
I'm trying to include Eggnog mapper in an Anvio workflow, but it stops with a non descriptive error. No clue if it's an issue with my workflow of with my install…
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## The dependency [stripe](https://github.com/stripe/stripe-node) was updated from `6.18.0` to `6.18.1`.
🚨 [View failing branch](https://github.com/greenkeeperio/greenkeeper/compare/master...greenke…
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toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/get_species_taxids/2.10.1+galaxy2
Connection fails but produces a green dataset with taxon id, red error with taxon name. Same error message.
`…
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I just want to put this out there before I change the required values for ALL READMEs in the datastore. Right now, the following are required across the board by all mine loaders: identifier, taxid, s…
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We should remove the reference genome field and replace it with an entry from the [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7408187/) resource.
The relevant information to store …
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Refactor code and/or tests to pass test runs
1. bte-server
- [x] updated workflow config
- [ ] all checks passing
3. api-response-transform
- [x] updated workflow config
- [x] …