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:cool:
### :pushpin: Explain the Request
Some GenBank accessions are unable to be downloaded via the command we currently have in the Assembly_fetch workflow:
```
datasets download genome ac…
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Hello, I hope you are well!
I'm able to download a specific NCBI Assembly via `bactopia --accession [accession]` -- is there a way to do so with a list of NCBI Assembly accessions (i.e bactopia --…
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I am getting error while running:
kraken2-build --standard --db kraken2_db
Error:
rsync: link_stat "/refseq/archaea/assembly_summary.txt" (in genomes) failed: No such file or directory (2)
rsync…
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Dear Dr. Davis JT,
I hope this message finds you well. My name is Daichunyan, and I am a student working in at NORTHWEST A&F UNIVERSITY. I recently came across your outstanding article titled "Whole-…
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Hi,
I got error message:
> annotations seqlevelsStyle(annotations)
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Hello,
I'm using the development version of SCENIC+.
When running the snakemake pipeline, it seems to get stuck on 'download_genome_annotations'...
Contents of my Snakemake folder:
-rw-r…
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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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**Is your feature request related to a problem? Please describe.**
I would like to be able to quickly determine what research article I should reference simply from looking at the output of `datasets…
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Sometimes one needs to analyze data that has been aligned against an old genome assembly. As far as I can see, there is no explicit direction in the documentation as to how the workflow should be modi…
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I try to download 204 agrobacterium assembly refseq from NCBI,
```python
DB_ID = "assembly"
term = "Agrobacterium[ORGN]"
# use esearch to retrieve a list of UIDs, later for efetch
search_hand…