Question: How to solve the elink error ?
0
gravatar for saadleeshehreen
21 months ago by
saadleeshehreen70 wrote:

Hi I am trying to get assembly number ( for example GCF_001166025.1 is for NZ_CQEB01000017.1) for 100 genomes with the following command. The command previously work for me but today giving some error. Anyone know what happen?

elink -db nuccore -id NZ_CQEB01000017.1 -target assembly|esummary|xtract -pattern DocumentSummary -element AssemblyAccession

501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)
No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi? dbfrom=nuccore&db=assembly&cmd=neighbor_history&linkname=nuccore_assembly&id=NZ_CQEB01000017.1&edirect_os=linux&edirect=10.2&tool=edirect
Result of do_post http request is
$VAR1 = bless( {
             '_request' => bless( {
                                    '_content' => 'dbfrom=nuccore&db=assembly&cmd=neighbor_history&linkname=nuccore_assembly&id=NZ_CQEB01000017.1&edirect_os=linux&edirect=10.2&tool=edirect&email=saadleeshehreen@biochemcompute.otago.ac.nz',
                                    '_uri' => bless( do{\(my $o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi')}, 'URI::https' ),
                                        '_headers' => bless( {
                                                           'user-agent' => 'libwww-perl/6.15',
                                                           'content-type' => 'application/x-www-form-urlencoded'
                                                         }, 'HTTP::Headers' ),
                                    '_method' => 'POST'
                                  }, 'HTTP::Request' ),
             '_msg' => 'Protocol scheme \'https\' is not supported (LWP::Protocol::https not installed)',
             '_rc' => 501,
             '_content' => 'LWP will support https URLs if the LWP::Protocol::https module
      is installed.
            ',
                      '_headers' => bless( {
                                    '::std_case' => {
                                                      'client-warning' => 'Client-Warning',
                                                      'client-date' => 'Client-Date'
                                                    },
                                    'client-warning' => 'Internal response',
                                    'client-date' => 'Thu, 28 Feb 2019 06:34:16 GMT',
                                    'content-type' => 'text/plain'
                                  }, 'HTTP::Headers' )
           }, 'HTTP::Response' );

     WebEnv value not found in link output - WebEnv1 
      Db value not found in summary input
elink ncbi • 419 views
ADD COMMENTlink written 21 months ago by saadleeshehreen70
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