<p><code>501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)</code> indicates that a specific perl module is missing.</p>
<p>If indeed your edirect installation is from March 2019 (as I interpret from <code>e-utilities/03.02.19</code>), you should update your edirect installation to the latest version. If you update, I expect the necessary perl module will be installed and the error will go away.</p>

CC BY-SA 4.0
2020-10-05T18:40:01.637Z
Ah! of course ... consider using CPAN to load the module
M__
CC BY-SA 4.0
2020-10-06T10:58:19.017Z
I just downloaded the script install-edirect.sh from this link ((https://www.ncbi.nlm.nih.gov/books/NBK179288/), then execute it by running:

source ./install-edirect.sh

and it works well!
Many thanks
bioinfonext
CC BY-SA 4.0
2020-10-05T16:59:02.777Z
2020-10-05T16:59:02.777Z
vkkodali
<p>I keep getting the error while using E-utilities on Slurm HPC, could you suggest how I can resolve it?</p>
<p>SCRIPT:</p>
<pre><code>#!/bin/bash
#SBATCH --job-name=tax_job_test      # Job name
#SBATCH --mail-type=END,FAIL         # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=na@gmail.com    # Where to send mail
#SBATCH --ntasks=8                  # Number of MPI ranks
#SBATCH --nodes=1                    # Number of nodes
#SBATCH --time=23:05:00              # Time limit hrs:min:sec
#SBATCH --partition=k2-medpri

module load e-utilities/03.02.19
module load apps/perl/5.20.2/gcc-4.8.5


for i in `cat taxonomy.id.txt` ; do efetch -db nuccore -format gbc -id ${i} |xtract  -pattern INSDSeq -element INSDSeq_accession-version INSDSeq_taxonomy INSDSeq_organism &gt;&gt;taxo.2020.txt; done
</code></pre>
<p>input <code>taxonomy.id.txt</code> is like this:</p>
<pre><code>AKN43077.1
AKN41814.1
PNE10086.1
AKN42672.1
AKN41654.2
AKN43077.1
PNE10086.1
AKN43189.1
TMK08501.1
TMK08501.1
AKN42976.1
AKN43189.1
AIZ47938.1
</code></pre>
<p>Error:</p>
<p>The script keep giving below error:</p>
<pre><code>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&amp;id=AKN43077.1
&amp;rettype=gbc&amp;retmode=xml&amp;edirect_os=linux&amp;edirect=11.7&amp;tool=edirect&amp;email=3052771@node126.pri.kelvin2.alces.network'

Result of do_post http request is

<span class="math-container">$VAR1 = bless( {
                 '_rc' =&gt; 501,
                 '_request' =&gt; bless( {
                                        '_method' =&gt; 'POST',
                                        '_uri' =&gt; bless( do{\(my $</span>o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi')}, 'URI::https' ),
                                        '_content' =&gt; 'db=nuccore&amp;id=AKN43077.1  
&amp;rettype=gbc&amp;retmode=xml&amp;edirect_os=linux&amp;edirect=11.7&amp;tool=edirect&amp;email=3052771@node126.pri.kelvin2.alces.network',
                                        '_headers' =&gt; bless( {
                                                               'content-type' =&gt; 'application/x-www-form-urlencoded',
                                                               'user-agent' =&gt; 'libwww-perl/6.39'
                                                             }, 'HTTP::Headers' )
                                      }, 'HTTP::Request' ),
                 '_content' =&gt; 'LWP will support https URLs if the LWP::Protocol::https module
is installed.
',
                 '_headers' =&gt; bless( {
                                        'client-warning' =&gt; 'Internal response',
                                        '::std_case' =&gt; {
                                                          'client-warning' =&gt; 'Client-Warning',
                                                          'client-date' =&gt; 'Client-Date'
                                                        },
                                        'client-date' =&gt; 'Mon, 05 Oct 2020 14:27:37 GMT',
                                        'content-type' =&gt; 'text/plain'
                                      }, 'HTTP::Headers' ),
</code></pre>
<p>Many thanks</p>

<phylogenetics><hpc><e-utilities>
Error while using E-utilities on slurm HPC
# Error while using E-utilities on slurm HPC

(Asked by: username_0 on 2020-10-05)

I keep getting the error while using E-utilities on Slurm HPC, could you suggest how I can resolve it?
SCRIPT:
#!/bin/bash
#SBATCH --job-name=tax_job_test      # Job name
#SBATCH --mail-type=END,FAIL         # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=na@gmail.com    # Where to send mail
#SBATCH --ntasks=8                  # Number of MPI ranks
#SBATCH --nodes=1                    # Number of nodes
#SBATCH --time=23:05:00              # Time limit hrs:min:sec
#SBATCH --partition=k2-medpri

module load e-utilities/03.02.19
module load apps/perl/5.20.2/gcc-4.8.5


for i in `cat taxonomy.id.txt` ; do efetch -db nuccore -format gbc -id ${i} |xtract  -pattern INSDSeq -element INSDSeq_accession-version INSDSeq_taxonomy INSDSeq_organism >>taxo.2020.txt; done

input taxonomy.id.txt is like this:
AKN43077.1
AKN41814.1
PNE10086.1
AKN42672.1
AKN41654.2
AKN43077.1
PNE10086.1
AKN43189.1
TMK08501.1
TMK08501.1
AKN42976.1
AKN43189.1
AIZ47938.1

Error:
The script keep giving below error:
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=AKN43077.1
&rettype=gbc&retmode=xml&edirect_os=linux&edirect=11.7&tool=edirect&email=3052771@node126.pri.kelvin2.alces.network'

Result of do_post http request is

$VAR1 = bless( {
                 '_rc' => 501,
                 '_request' => bless( {
                                        '_method' => 'POST',
                                        '_uri' => bless( do{\(my $o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi')}, 'URI::https' ),
                                        '_content' => 'db=nuccore&id=AKN43077.1  
&rettype=gbc&retmode=xml&edirect_os=linux&edirect=11.7&tool=edirect&email=3052771@node126.pri.kelvin2.alces.network',
                                        '_headers' => bless( {
                                                               'content-type' => 'application/x-www-form-urlencoded',
                                                               'user-agent' => 'libwww-perl/6.39'
                                                             }, 'HTTP::Headers' )
                                      }, 'HTTP::Request' ),
                 '_content' => 'LWP will support https URLs if the LWP::Protocol::https module
is installed.
',
                 '_headers' => bless( {
                                        'client-warning' => 'Internal response',
                                        '::std_case' => {
                                                          'client-warning' => 'Client-Warning',
                                                          'client-date' => 'Client-Date'
                                                        },
                                        'client-date' => 'Mon, 05 Oct 2020 14:27:37 GMT',
                                        'content-type' => 'text/plain'
                                      }, 'HTTP::Headers' ),

Many thanks

**Tags:** phylogenetics, hpc, e-utilities

---

## 1 answers

### Answer by username_1 on 2020-10-05. Score: 2 | Accepted answer

`501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)` indicates that a specific perl module is missing.

If indeed your edirect installation is from March 2019 (as I interpret from `e-utilities/03.02.19`), you should update your edirect installation to the latest version. If you update, I expect the necessary perl module will be installed and the error will go away.

> **Comments:**
> **username_2**: Ah! of course ... consider using CPAN to load the module  
> **username_0**: I just downloaded the script install-edirect.sh from this link ((https://www.ncbi.nlm.nih.gov/books/NBK179288/), then execute it by running:  source ./install-edirect.sh  and it works well! Many thanks  

---

