Unable to download anything but fna files

[chasemc]

datasets version: 3.42.1

command: datasets download genome accession GCA_000302695.1 --include-gbff

Results:

├── ncbi_dataset
│   └── data
│       ├── assembly_data_report.jsonl
│       ├── dataset_catalog.json
│       └── GCA_000302695.1
│           ├── GCA_000302695.1_LSJC7_1.0_genomic.fna
│           └── sequence_report.jsonl
└── README.md

[mtntsuchiya]

Hi chasemc, Thanks for letting us know about this issue and I'm sorry about it.

I was able to replicate the error and our team is looking for a solution. In the meantime, you can find the gbff file for that assembly in our FTP site: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/302/695/GCA_000302695.1_LSJC7_1.0/GCA_000302695.1_LSJC7_1.0_genomic.gbff.gz. You can use wget to retrieve the file:

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/302/695/GCA_000302695.1_LSJC7_1.0/GCA_000302695.1_LSJC7_1.0_genomic.gbff.gz

We'll keep you posted on the solution of this issue.

Thanks again,

Mirian T. N. Tsuchiya, Ph.D. Bioinformatics Data Wrangler (contractor) NCBI Datasets (NCBI/NLM/NIH) (she/her/hers)

[chasemc]

Sorry to ask here, but where should we report bugs in the online interfaces?

[ericcox1]

Hi Chase,

Feel free to open a new issue here on our GitHub page to report any bugs in our online (web) interfaces, CLI tools, or API.

Best, Eric

Eric Cox, PhD [Contractor] (he/him/his) NCBI Datasets Sequence Enhancements, Tools and Delivery (SeqPlus) NIH/NLM/NCBI [email protected]

[chasemc]

Hi Chase,

Feel free to open a new issue here on our GitHub page to report any bugs in our online (web) interfaces, CLI tools, or API.

Best, Eric

Eric Cox, PhD [Contractor] (he/him/his) NCBI Datasets Sequence Enhancements, Tools and Delivery (SeqPlus) NIH/NLM/NCBI [email protected]

Thanks, the online interface bug seems to have mysteriously resolved but I'll keep that in mind

[chasemc]

@mtntsuchiya Thanks, I needed to selectively download data for a large number of genomes, this was just a minimal example. I'll wait for now and concoct something with eutils if I need to