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grybnicky / Spacer2PAM

This repository contains the source code for the R package Spacer2PAM, which is used to guide experimental determination of functional PAM sequences from CRISPR array spacers.
GNU General Public License v3.0
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Failed to connect to eutils.ncbi.nlm.nih.gov #4

Open ireneortega opened 1 year ago

ireneortega commented 1 year ago

I am working with a joineddata df that contains many rows and the funtion join2PAM() stops after long time due to this error:

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [eutils.ncbi.nlm.nih.gov] Failed to connect to eutils.ncbi.nlm.nih.gov port 443 after 5199 ms: Couldn't connect to server
Calls: join2PAM ... request_fetch -> request_fetch.write_memory -> <Anonymous>

How can I fix it?

grybnicky commented 1 year ago

This is a problem with NCBI's server capacity. Unfortunately, they cap the size and time of requests via API. Have you tried running this one manually through the BLAST web interface?

ireneortega commented 1 year ago

Could you please tell me how can I perform the function join2PAM() manually? Do I have to download the fasta sequences for the IDs in joineddata$subject.acc.ver in one file and add this file to the eFetchGet object (line 330 join2PAM.R)?

ireneortega commented 1 year ago

@grybnicky I propose you a modification in the function join2PAM() that avoid NCBI's server capacity. It works for my data, hope it is correct

grybnicky commented 1 year ago

Thanks for proposing the modification, I just need time to verify it before I accept it. Do you have a reproducible example I can use to test? Feel free to email it to me.