Possibility to supply NCBI API key when running pipeline to access NCBI data faster?

[janstrauss1]

Hi there,

thanks for your efforts developing phylotaR!

Unfortunately, I'm encountering issues when trying to run phylotaR for larger taxonomic groups (e. g. txid=33630). It happens during the download stage when fetching data from NCBI:

taxise_run(wd = wd)
download_run(wd = wd)

after downloading some part of the data I get

Retrying in [1s] for [fetch]
Retrying in [3s] for [fetch]
Retrying in [6s] for [fetch]
Retrying in [10s] for [fetch]
Retrying in [60s] for [fetch]
Retrying in [300s] for [fetch]
Retrying in [300s] for [fetch]
Retrying in [300s] for [fetch]
...

I therefore wondered if its possible to set a NCBI API key to access the NCBI data faster as described in this blog post https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/?

Many thanks in advance for your help!

Jan

[bheimbu]

Hi,

I got also stuck at the downloading stage (Taxid: 48704). Any thoughts on implementing a NCBI API key?

Cheers Bastian