How to avoid timeout while downloading from NCBI
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!
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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?
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)
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.