To download the sequences by using NCBI entrenz direct

Question

[bandanaschapagain]

Hi all,

I am stuck with something that is simple for most of you all. I have list of NCI_Acession Number for downloading the genome from NCBI. I am using NCBI entrenz to get the data. The command I am using for testing if or not I downloaded the entrenz edirect successfully I used the command:

esearch -db nucleotide -query "NC_001552" | efetch -format fasta > output.fasta

The error I am getting says,

connect attempt failed.
Result of do_post http request is
$VAR1 = bless( {
                 '_content' => 'Can\'t connect to eutils.be-md.ncbi.nlm.nih.gov:443 (certificate verify failed)

I am trying to fix it but I am not able to. Can anyone help me with this? Regards, Bandana

[GenoMax]

Are you using the latest edirect utils release? NCBI has switched to HTTPS only connections.

[bandanaschapagain]

Yes. I downloaded from Ncbi site

[GenoMax]

I am also getting an error but a different one. In your case it looks like the SSL cert on eutils.be-md.ncbi.nlm.nih.gov error.

Edit: I am not 100% certain if the error is on our end or NCBI's. They appear to be using a wildcard SSL cert on their end.

[Sej Modha]

Unable to replicate the error and the command works for me. I am using eutils version 4.80

[GenoMax]

It appears that edirect now needs a newer version of OpenSSL. OpenSSL 1.0.1k 8 is working for me. Check with your sys admins to see if upgrading OpenSSL is a possibility.

Answer 1

[usachu]

Try setting path of HTTPS_CA_DIR. In case of my environment (Ubuntu), the path is /etc/ssl/certs.

Insert the following line after 'BEGIN{' (L44) in edirect.pl

  $ENV{HTTPS_CA_DIR} = '/etc/ssl/certs';

Reference at stackoverflow

I hope this helps.

[rc.silva]

This works (2019-02)! Thank you!