Question: efetch error LWP::Protocol::https not installed
0
gravatar for traviata
14 months ago by
traviata0
traviata0 wrote:

I'm trying to use fetch to download a sequence. However, I keep on getting 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed) even though I have ran sudo cpan install LWP::Protocol::https

The terminal output is as follows:

$ efetch -db nuccore -id AF086833 -format fasta
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/efetch.fcgi?db=nuccore&id=AF086833&rettype=fasta&retmode=text&edirect=7.00&tool=edirect&email=kjsdhjasv@MacBook-Air.local'
Result of do_post http request is
$VAR1 = bless( {
                 '_rc' => 501,
                 '_content' => 'LWP will support https URLs if the LWP::Protocol::https module
is installed.
',
                 '_msg' => 'Protocol scheme \'https\' is not supported (LWP::Protocol::https not installed)',
                 '_request' => bless( {
                                        '_method' => 'POST',
                                        '_content' => 'db=nuccore&id=AF086833&rettype=fasta&retmode=text&edirect=7.00&tool=edirect&email=kjsdhjasv@MacBook-Air.local',
                                        '_uri' => bless( do{\(my $o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi')}, 'URI::https' ),
                                        '_headers' => bless( {
                                                               'content-type' => 'application/x-www-form-urlencoded',
                                                               'user-agent' => 'libwww-perl/6.26'
                                                             }, 'HTTP::Headers' )
                                      }, 'HTTP::Request' ),
                 '_headers' => bless( {
                                        'client-warning' => 'Internal response',
                                        'content-type' => 'text/plain',
                                        '::std_case' => {
                                                          'client-warning' => 'Client-Warning',
                                                          'client-date' => 'Client-Date'
                                                        },
                                        'client-date' => 'Mon, 02 Oct 2017 15:56:40 GMT'
                                      }, 'HTTP::Headers' )
               }, 'HTTP::Response' );
efetch • 1.5k views
ADD COMMENTlink modified 12 weeks ago by Jinguo10 • written 14 months ago by traviata0

I am unable to replicate the error, are you sure that the edirect eutils are installed properly?

ADD REPLYlink written 14 months ago by Sej Modha3.9k

Probably conflict of Perl versions. What is the result of

which perl

and

head -n1 $(which efetch)
ADD REPLYlink written 14 months ago by h.mon22k
3
gravatar for tarek.mohamed
14 months ago by
tarek.mohamed190
tarek.mohamed190 wrote:

Hi,

How did you install Entrez direct tool?

This is due to a mistake in the installation of Entrez direct tool. Try this code to install it!

mkdir -p ~/src 
curl https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip > ~/src/edirect.zip 
unzip -o ~/src/edirect.zip  -d ~/src 
echo 'export PATH=~/src/edirect:$PATH' >> ~/.bashrc 
source  ~/.bashrc

Tarek

ADD COMMENTlink modified 14 months ago • written 14 months ago by tarek.mohamed190

Your solution worked. Thanks so much!

ADD REPLYlink written 14 months ago by traviata0
1
gravatar for Jinguo
12 weeks ago by
Jinguo10
Jinguo10 wrote:

I met the same problem when I use efetch, but the given solutions didn't work out.

I tried

cpanm Crypt::SSLeay IO::Socket::SSL::Utils LWP::Protocol::https

and it worked!

ADD COMMENTlink written 12 weeks ago by Jinguo10
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