Unable to download the Influenza A taxon assembly

[anna-parker]

Describe the bug

Hi! I'm having trouble downloading all influenza A assemblies, I have been downloading for over 3hours and am not yet finished - previously the download was interrupted twice after 2h with a message: "Connection reset by peer". As of today I have been unable to download the dataset. I have been trying to download it using:

datasets download genome taxon 11320 --assembly-source genbank  --filename genbank_assembly.zip

To Reproduce
Run

datasets download genome taxon 11320 --assembly-source genbank  --filename genbank_assembly.zip

Expected behavior
I understand that this is a very large folder, so I do expect the download to take time - it there perhaps a way to batch this and not have the download fail after 2hours?

For context I am able to download all influenza A samples in ~10min using

datasets download virus genome taxon 11320 --filename data.zip

I am also able to download all assemblies from refseq just not genbank

datasets download genome taxon 11320 --assembly-source refseq  --filename refseq_assembly.zip

Thank you

Thanks for your feedback--your bug reports help improve NCBI Datasets.

[mtntsuchiya]

Hi Anna,
Thank you for letting us know of this issue. I'm looking into it now and I'll let you know what I find.
Thanks,
Mirian

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

[syntheticgio]

We are able to replicate the problem @anna-parker, currently investigating what might be the underlying cause.

[anna-parker]

Thanks! I am connecting from Switzerland - so maybe its a location issue? I tried downloading from my home and from work today and saw similar results. My internet speed at home isn't great but speed tests show I have 17.8 Mbps download.

[ericcox1]

Hi @anna-parker,

Have you tried using rehydration? This should speed up the download.

For example, to download influenza A assemblies:

datasets download genome taxon 11320 --assembly-source genbank --dehydrated  --filename genbank_assembly.zip
unzip genbank_assembly.zip -d genbank_assembly
datasets rehydrate --directory genbank_assembly

Best,
Eric

[anna-parker]

@ericcox1 thank you so much for this suggestion! I tested it now and it took me 1h27m to download but the download was successful!!! I'm so excited to get a closer look at the data!