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Unexpected EOF Errors During Actinopterygii Genomes Download in RefSeq

16

#### Background: Encountered multiple `unexpected EOF` errors while attempting to download the RefSeq genomes of Actinopterygii (taxon id: 7898) using `datasets` version 15.30.0. #### Steps to Reproduce: 1. **Initial Download...

mkrg01

Include md5sum in JSON or as other output

1

Hi, Thank you for your team's commendable work on `datasets` which finally provides a comprehensive and singular way to download data from NCBI, whereas previously one had to resort to...

aboffin

Truncated FNAs on non-dehydrated downloads of large datasets, please make it more clear that non-dehydrated downloads are dangerous

1

When using `datasets` to download a large collection of genomes, many of the associated ```.fna``` files are silently truncated. I was fortunate in that: 1) a few of the files...

joeweaver

--geo-location flag runs into invalid zip archive error

3

Hi NCBI Datasets team, Today I've tried a couple geolocations with the `--geo-location` flag and have run into the `invalid zip archive` error every time. My attempt with state level...

joverlee521

404 on annotation_report when assembly has no annotations

2

Somewhat similar to #312. In this case, I don't really know what the ideal response should be, but I was suprised to get a 404 when requesting annotations from an...

manulera

taxon_suggest endpoint does not return E. coli species (taxid:562)

1

I noticed that the taxon_suggest endpoint does not return the E. coli species (taxid:562), only some strains of the species. https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon_suggest/Escherichia%20coli Is there a reason for this? I noticed that...

manulera

Host mirror of the datasets cli code here

3

I've noticed that this repo doesn't contain the source code - to get the source code one needs to look at the release artefacts. Is there a reason you are...

corneliusroemer

--include none and --chromosomes all

4

Hello, I would like to use the `--chromosomes all` option when I download a genome to only get the chromosomes. I noticed that using this option also automatically downloads the...

conchoecia

Not all parameters of the taxonomy API work

3

https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon/9606?returned_content=COMPLETE and https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon/9606?returned_content=TAXIDS both return the same output. Should there be no difference between the two? The parameters under `filtered_subtree` also seem to have little effect.

alvanuffelen

correct headers for tab-delimited output

1

Hi, The OpenAPI spec indicates that tab-delimited data can be returned for some endpoints by using the `Allow: x-tabular` header. The demo on the API docs site, however, uses `Allow:...

jvolkening