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To download the sequences by using NCBI entrenz direct

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

rna-seq genome sequencing ncbi entrez
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updated by Andrzej Zielezinski Andrzej Zielezinski • written by bandanaschapagain • bandanaschapagain

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

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written by GenoMax 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.

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written by GenoMax GenoMax

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

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written by Sej Modha Sej Modha

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.

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written by GenoMax GenoMax

1 answer

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.

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written by usachu • usachu

This works (2019-02)! Thank you!

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written by rc.silva • rc.silva

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