How to avoid timeout while downloading from NCBI

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6.2 years ago

Selina ▴ 10

Hi everyone,

I am trying to download all fungal sequences from the NCBI nucleotide databank using Entrez Direct. My command looks like this:

esearch -db nuccore -query fungi[organism] | efetch -format fasta > fungi_db

Basically this works but I always get an error saying:

Error: External viewer error: Empty Response. Bytes read: 0 Status: Timeout

How do I avoid this? Has anyone experience with this?

Thanks in advance for any help!

NCBI Entrez Direct • 3.4k views

ADD COMMENT • link updated 6.2 years ago by Ram 43k • written 6.2 years ago by Selina ▴ 10

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use an api_key https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ , check the proxy settings (if any)

ADD REPLY • link 6.2 years ago by Pierre Lindenbaum 161k

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API keys will be required after May 1, 2018 so for now they should not be causing this issue. But getting ready for that would be a good thing.

ADD REPLY • link 6.2 years ago by GenoMax 141k

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Could this be a limitation of your local internet bandwidth (and/or local packet inspection/intrusion prevention devices) since NCBI is unlikely to have a problem serving this data to you?

ADD REPLY • link 6.2 years ago by GenoMax 141k

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