Answers.Body: <p>I think it is quite simple you need to install <code>perlbrew</code> <a href="https://perlbrew.pl/" rel="nofollow noreferrer">here</a></p>
  <p>You then run the software under perlbrew it should work.</p>
  <p>At present you are running the system perl5 and that is causing all sorts issues, for example the age of the installation and the fact system operations and your software are using the same version of perl.</p>
  <p>All the instructions are in the website link.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-05T13:42:30.833Z
Answers.Text: Actually I'd recommend Anaconda/conda now.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-13T09:29:40.040Z
Answers.LastActivityDate: 2020-11-13T09:29:40.040Z
Answers.UserDisplayName: M__
Body: <p>I'm trying to run Repeatmasker in Linux on the command line with:</p>
  <pre><code>./RepeatMasker -species human -alu -gff -dir /mnt/lustre/users/Analysis/RepeatMaskerOutput /mnt/lustre/users/Software/STAR/bin/Linux_x86_64/HRG_Newest_and_Annotation/GCA_000001405.28_GRCh38.p13_genomic.fna
  </code></pre>
  <p>but I am getting this error:</p>
  <pre class="lang-none prettyprint-override"><code>perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = &quot;en_GB.utf8&quot;,
          LC_ALL = &quot;&quot;,
          LC_CTYPE = &quot;en_GB.utf8&quot;,
          LANG = &quot;en_GB.utf8&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  RepeatMasker version open-4.0.9
  TRF program not configured! This version of RepeatMasker requires a
  local installatoin of TRF.  Please visit:
                 http://tandem.bu.edu/trf/trf.html
  to obtain the current version.  Once installed please re-run the
  RepeatMasker configure script to setup RepeatMasker to use the new
  installation. at ./RepeatMasker line 442.
  </code></pre>
  <p>I have downloaded rmBlast and the latest TRF file. I have put the TRF file in my <code>Users/username/bin</code> PATH folder and used <code>chmod a+x</code> (and <code>chmod 755</code>) on it. I then changed my <code>LD_LIBRARY_PATH</code> using <code>export</code> to my glibc directory.</p>
  <p>After this I used <code>perl ./configure</code> and directed the program to the PATH folder where the TRF file was. It gave a series of the same error messages as above but was 'successful' as shown here:</p>
  <pre><code>
  [user@nodec23() RepeatMasker]$ perl ./configure
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  RepeatMasker Configuration Program
  
  **TRF PROGRAM**
  
    This is the full path to the TRF program.
   This is now used by RepeatMasker to mask simple repeats.
  
  Enter path  [ /mnt/lustre/users/Software/RepeatMasker/RepeatMasker/TRF.pm ]
  
  Add a Search Engine:
     1. Crossmatch - Phrap             [ Configured ]
     2. RMBlast - Improved NCBI Blast  [ Configured, Default ]
     3. HMMER3.1 &amp; DFAM                [ Un-configured ]
     4. ABBlast/WUBlast                [ Un-configured ]
     5. Done
  
  Enter Selection: 5
   -- Setting perl interpreter...
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  
  Congratulations!  RepeatMasker is now ready to use.
  The program is installed with a the following repeat libraries:
    Dfam database version Dfam_3.0
    RepeatMasker Combined Database: Dfam_3.0
  Further documentation on the program may be found here:
    /mnt/lustre/users/Software/RepeatMasker/RepeatMasker/repeatmasker.help
  </code></pre>
  <p>I'm at a loss of what to do next. I have googled and tried changing each of the locale settings with export to the following:</p>
  <ul>
  <li>en_GB</li>
  <li>en_US.utf8</li>
  <li>en_GB:2000</li>
  <li>en_GB.utf8</li>
  </ul>
  <p>but none have changed the error.</p>
  <p>I am running a Windows 10 machine and using PuTTY to connect to an HPC which uses a Linux environment.</p>
  <p>Locale settings are as follows:</p>
  <pre><code>locale: Cannot set LC_CTYPE to default locale: No such file or directory
  locale: Cannot set LC_MESSAGES to default locale: No such file or directory
  locale: Cannot set LC_ALL to default locale: No such file or directory
  LANG=en_GB
  LC_CTYPE=&quot;en_GB&quot;
  LC_NUMERIC=&quot;en_GB&quot;
  LC_TIME=&quot;en_GB&quot;
  LC_COLLATE=&quot;en_GB&quot;
  LC_MONETARY=&quot;en_GB&quot;
  LC_MESSAGES=&quot;en_GB&quot;
  LC_PAPER=&quot;en_GB&quot;
  LC_NAME=&quot;en_GB&quot;
  LC_ADDRESS=&quot;en_GB&quot;
  LC_TELEPHONE=&quot;en_GB&quot;
  LC_MEASUREMENT=&quot;en_GB&quot;
  LC_IDENTIFICATION=&quot;en_GB&quot;
  LC_ALL=
  </code></pre>
  <p>Also please note that I do not have administrator access.</p>
  <p>Typing 'perl -v' gives the following:</p>
  <pre><code>perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = &quot;en_GB&quot;
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale (&quot;C&quot;).
  
  This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi
  
  Copyright 1987-2009, Larry Wall
  
  Perl may be copied only under the terms of either the Artistic License or the
  GNU General Public License, which may be found in the Perl 5 source kit.
  
  Complete documentation for Perl, including FAQ lists, should be found on
  this system using &quot;man perl&quot; or &quot;perldoc perl&quot;.  If you have access to the
  Internet, point your browser at http://www.perl.org/, the Perl Home Page.
  </code></pre>
  <p>Typing &quot;LC_ALL=C perl ./configure&quot; and going throught the configurations leads to the same outcome but without the perl errors:</p>
  <pre><code>Enter Selection: 5
   -- Setting perl interpreter...
  
  Congratulations!  RepeatMasker is now ready to use.
  The program is installed with a the following repeat libraries:
    Dfam database version Dfam_3.0
    RepeatMasker Combined Database: Dfam_3.0
  Further documentation on the program may be found here:
    /mnt/lustre/users/k1894998/Software/RepeatMasker/RepeatMasker/repeatmasker.help
  
  </code></pre>
  <p>However, the error remains when trying to run Repeatmasker.</p>
  
Tags: <rna-seq><perl><linux><repeatmasker>
Title: "perl: warning: Setting locale failed." in RepeatMasker
ThreadText: # "perl: warning: Setting locale failed." in RepeatMasker
  
  (Asked by: username_0 on 2019-06-26)
  
  I'm trying to run Repeatmasker in Linux on the command line with:
  
  ```
  ./RepeatMasker -species human -alu -gff -dir /mnt/lustre/users/Analysis/RepeatMaskerOutput /mnt/lustre/users/Software/STAR/bin/Linux_x86_64/HRG_Newest_and_Annotation/GCA_000001405.28_GRCh38.p13_genomic.fna
  
  ```
  
  but I am getting this error:
  
  ```none
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = "en_GB.utf8",
          LC_ALL = "",
          LC_CTYPE = "en_GB.utf8",
          LANG = "en_GB.utf8"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  RepeatMasker version open-4.0.9
  TRF program not configured! This version of RepeatMasker requires a
  local installatoin of TRF.  Please visit:
                 http://tandem.bu.edu/trf/trf.html
  to obtain the current version.  Once installed please re-run the
  RepeatMasker configure script to setup RepeatMasker to use the new
  installation. at ./RepeatMasker line 442.
  
  ```
  
  I have downloaded rmBlast and the latest TRF file. I have put the TRF file in my `Users/username/bin` PATH folder and used `chmod a+x` (and `chmod 755`) on it. I then changed my `LD_LIBRARY_PATH` using `export` to my glibc directory.
  
  After this I used `perl ./configure` and directed the program to the PATH folder where the TRF file was. It gave a series of the same error messages as above but was 'successful' as shown here:
  
  ```
  
  [user@nodec23() RepeatMasker]$ perl ./configure
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  RepeatMasker Configuration Program
  
  **TRF PROGRAM**
  
    This is the full path to the TRF program.
   This is now used by RepeatMasker to mask simple repeats.
  
  Enter path  [ /mnt/lustre/users/Software/RepeatMasker/RepeatMasker/TRF.pm ]
  
  Add a Search Engine:
     1. Crossmatch - Phrap             [ Configured ]
     2. RMBlast - Improved NCBI Blast  [ Configured, Default ]
     3. HMMER3.1 & DFAM                [ Un-configured ]
     4. ABBlast/WUBlast                [ Un-configured ]
     5. Done
  
  Enter Selection: 5
   -- Setting perl interpreter...
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  
  Congratulations!  RepeatMasker is now ready to use.
  The program is installed with a the following repeat libraries:
    Dfam database version Dfam_3.0
    RepeatMasker Combined Database: Dfam_3.0
  Further documentation on the program may be found here:
    /mnt/lustre/users/Software/RepeatMasker/RepeatMasker/repeatmasker.help
  
  ```
  
  I'm at a loss of what to do next. I have googled and tried changing each of the locale settings with export to the following:
  
  * en\_GB
  * en\_US.utf8
  * en\_GB:2000
  * en\_GB.utf8
  
  but none have changed the error.
  
  I am running a Windows 10 machine and using PuTTY to connect to an HPC which uses a Linux environment.
  
  Locale settings are as follows:
  
  ```
  locale: Cannot set LC_CTYPE to default locale: No such file or directory
  locale: Cannot set LC_MESSAGES to default locale: No such file or directory
  locale: Cannot set LC_ALL to default locale: No such file or directory
  LANG=en_GB
  LC_CTYPE="en_GB"
  LC_NUMERIC="en_GB"
  LC_TIME="en_GB"
  LC_COLLATE="en_GB"
  LC_MONETARY="en_GB"
  LC_MESSAGES="en_GB"
  LC_PAPER="en_GB"
  LC_NAME="en_GB"
  LC_ADDRESS="en_GB"
  LC_TELEPHONE="en_GB"
  LC_MEASUREMENT="en_GB"
  LC_IDENTIFICATION="en_GB"
  LC_ALL=
  
  ```
  
  Also please note that I do not have administrator access.
  
  Typing 'perl -v' gives the following:
  
  ```
  perl: warning: Setting locale failed.
  perl: warning: Please check that your locale settings:
          LANGUAGE = (unset),
          LC_ALL = (unset),
          LANG = "en_GB"
      are supported and installed on your system.
  perl: warning: Falling back to the standard locale ("C").
  
  This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi
  
  Copyright 1987-2009, Larry Wall
  
  Perl may be copied only under the terms of either the Artistic License or the
  GNU General Public License, which may be found in the Perl 5 source kit.
  
  Complete documentation for Perl, including FAQ lists, should be found on
  this system using "man perl" or "perldoc perl".  If you have access to the
  Internet, point your browser at http://www.perl.org/, the Perl Home Page.
  
  ```
  
  Typing "LC\_ALL=C perl ./configure" and going throught the configurations leads to the same outcome but without the perl errors:
  
  ```
  Enter Selection: 5
   -- Setting perl interpreter...
  
  Congratulations!  RepeatMasker is now ready to use.
  The program is installed with a the following repeat libraries:
    Dfam database version Dfam_3.0
    RepeatMasker Combined Database: Dfam_3.0
  Further documentation on the program may be found here:
    /mnt/lustre/users/k1894998/Software/RepeatMasker/RepeatMasker/repeatmasker.help
  
  ```
  
  However, the error remains when trying to run Repeatmasker.
  
  **Tags:** rna-seq, perl, linux, repeatmasker
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-11-13. Score: 0
  
  I think it is quite simple you need to install `perlbrew` [here](https://perlbrew.pl/)
  
  You then run the software under perlbrew it should work.
  
  At present you are running the system perl5 and that is causing all sorts issues, for example the age of the installation and the fact system operations and your software are using the same version of perl.
  
  All the instructions are in the website link.
  
  > **Comments:**
  > **username_1**: Actually I'd recommend Anaconda/conda now.  
  
  ---
  
  