Entering edit mode
6.6 years ago
age00
•
0
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=age87@lg-1r17-n04.guillimin.clumeq.ca'
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=age87@lg-1r17-n04.guillimin.clumeq.ca',
'_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!
In case you didn't have a network problem, this would be the error message: