Using NCBIs EDirect to download mammalian refseq_rna database

Question

[age00]

I want to download the mammalian refseq_rna database using NCBI's EDirect on the command line in order to do a blastn query for 150,000 sequences (evidently too large for -remote)

This is what I have done:

esearch -db refseq_rna -query "mammalia [ORGN]" | efetch -format fasta  > mammalrefseq_rna.fsa

But I get this error:

500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (connect: Network is unreachable)
No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=refseq_rna&term=mammalia%20%5BORGN%5D&                                                                                            retmax=0&usehistory=y&edirect=7.20&tool=edirect&email=[e-mail]'
Result of do_post http request is
$VAR1 = bless( {
                 '_content' => '500 Can\'t connect to eutils.ncbi.nlm.nih.gov:443 (connect: Network is unreachable)
',
                 '_rc' => 500,
                 '_headers' => bless( {
                                        'client-warning' => 'Internal response',
                                        'client-date' => 'Tue, 29 Aug 2017 18:41:05 GMT',
                                        'content-type' => 'text/plain'
                                      }, 'HTTP::Headers' ),
                 '_msg' => 'Can\'t connect to eutils.ncbi.nlm.nih.gov:443 (connect: Network is unreachable)',
                 '_request' => bless( {
                                        '_content' => 'db=refseq_rna&term=mammalia%20%5BORGN%5D&retmax=0&usehistory=y&edirect=7.20&to                                                                                            ol=edirect&email=[e-mail]',
                                        '_uri' => bless( do{\(my $o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi')},                                                                                             'URI::https' ),
                                        '_headers' => bless( {
                                                               'user-agent' => 'libwww-perl/5.833',
                                                               'content-type' => 'application/x-www-form-urlencoded'
                                                             }, 'HTTP::Headers' ),
                                        '_method' => 'POST'
                                      }, 'HTTP::Request' )
               }, 'HTTP::Response' );

WebEnv value not found in search output - WebEnv1

Any help is greatly appreciated!

Answer 1

[Istvan Albert]

Your command fails because of network error so it never gets to submitting it.

In addition, the refseq_rna is not a valid database to esearch so it would not work even if the network error did not present itself. See:

einfo --dbs

for valid databases.

I would recommend to look at RNA Central and get data from there

http://rnacentral.org/

[h.mon]

In case you didn't have a network problem, this would be the error message:

ERROR in search output: Invalid db name specified: refseq_rna URL:
db=refseq_rna&term=mammalia%20%5BORGN%5D&retmax=0&usehistory=y

ERROR in fetch input: Invalid db name specified: refseq_rna

Answer 2

[GenoMax]

Following seems to be working.

esearch -db nuccore -query "mammalia [ORGN] AND srcdb refseq validated [PROP]" | efetch -format fasta > mammalian.fa