Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-05T18:40:01.637Z
Answers.Text: Ah! of course ... consider using CPAN to load the module
Answers.UserDisplayName: M__
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Answers.CreationDate: 2020-10-06T10:58:19.017Z
Answers.Text: 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
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Answers.UserDisplayName: vkkodali
Body: <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>
  
Tags: <phylogenetics><hpc><e-utilities>
Title: Error while using E-utilities on slurm HPC
ThreadText: # 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  
  
  ---
  
  