Question: efetch error LWP::Protocol::https not installed
1
gravatar for traviata
2.7 years ago by
traviata10
traviata10 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 • 3.6k views
ADD COMMENTlink modified 15 months ago by indexofire30 • written 2.7 years ago by traviata10

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

ADD REPLYlink written 2.7 years ago by Sej Modha4.7k

Probably conflict of Perl versions. What is the result of

which perl

and

head -n1 $(which efetch)
ADD REPLYlink written 2.7 years ago by h.mon29k

I've installed all the conda packages in your list. It still pop out the error msg. any ideas?

ADD REPLYlink written 15 months ago by indexofire30
7
gravatar for tarek.mohamed
2.7 years ago by
tarek.mohamed260
tarek.mohamed260 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 2.7 years ago • written 2.7 years ago by tarek.mohamed260

Your solution worked. Thanks so much!

ADD REPLYlink written 2.7 years ago by traviata10
3
gravatar for Liam Thompson
15 months ago by
Liam Thompson140
Gothenburg, Sweden
Liam Thompson140 wrote:

For those who have installed entrez-direct using Conda virtual environment, and are encountering the error above, you can install the libraries in the following way into the already activated virtual environment.

conda install perl-io-socket-ssl perl-net-ssleay perl-lwp-protocol-https entrez-direct
ADD COMMENTlink written 15 months ago by Liam Thompson140

add -c bioconda if bioconda is not in your channels already

ADD REPLYlink modified 14 months ago • written 14 months ago by russel26200
2
gravatar for Jinguo
20 months ago by
Jinguo20
Jinguo20 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 modified 12 days ago by RamRS27k • written 20 months ago by Jinguo20
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