Answers.Body: <p>You might prefer to run <a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html" rel="nofollow noreferrer">VEP</a> in offline mode:</p>
  <blockquote>
  <p>Using <code>--cache</code> (without <code>--offline</code>) uses the local cache on disk to
  fetch most annotations, but allows database connections for some
  features (see <a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations" rel="nofollow noreferrer">cache limitations</a>)</p>
  </blockquote>
  <p>If you need HGVS names in your output, you'll also need to supply a FASTA file using <code>--fasta</code>:</p>
  <blockquote>
  <p><a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_offline" rel="nofollow noreferrer">--offline</a></p>
  <p>Enable offline mode. No database connections will be made, and a cache file or GFF/GTF file is required for annotation. Add
  --refseq to use the refseq cache (if installed). Not used by default.</p>
  </blockquote>
  <blockquote>
  <p><a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_fasta" rel="nofollow noreferrer">--fasta [file|dir]</a></p>
  <p>Specify a FASTA file or a directory containing FASTA files to use to look up reference sequence. The first time you run VEP with this parameter an index will be built which can take a few minutes. This is required if fetching HGVS annotations (--hgvs) or checking reference sequences (--check_ref) in offline mode (--offline), and optional with some performance increase in cache mode (--cache). See documentation for more details. Not used by default.</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-11-12T04:15:36.827Z
Answers.LastActivityDate: 2021-11-12T04:15:36.827Z
Answers.UserDisplayName: Steve
Body: <p>I got this error during execution, pls guide me.</p>
  <pre><code>vep --cache -i xxxx.vcf -o xxxxx_new.vcf
  
  Possible precedence issue with control flow operator at /software/xxxx_pkgs/envs/ensemble-vep/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
  DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110) at /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/Bio/EnsEMBL/Registry.pm line 1771.
  
  -------------------- EXCEPTION --------------------
  MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings &amp; DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110)
  STACK Bio::EnsEMBL::Registry::load_registry_from_db /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/Bio/EnsEMBL/Registry.pm:1771
  STACK Bio::EnsEMBL::VEP::BaseVEP::registry /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:163
  STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:80
  STACK Bio::EnsEMBL::VEP::Runner::init /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/modules/Bio/EnsEMBL/VEP/Runner.pm:72
  STACK Bio::EnsEMBL::VEP::Runner::run /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/modules/Bio/EnsEMBL/VEP/Runner.pm:111
  STACK toplevel /software//envs/ensemble-vep/bin/vep:209
  Ensembl API version = 88
  <span class="math-container">```</span>
  </code></pre>
  
Tags: <vcf><sequence-annotation><ensembl><errors>
Title: Ensembl Variant Effect Predictor (VEP) issue during execution
ThreadText: # Ensembl Variant Effect Predictor (VEP) issue during execution
  
  (Asked by: username_0 on 2021-11-11)
  
  I got this error during execution, pls guide me.
  
  ```
  vep --cache -i xxxx.vcf -o xxxxx_new.vcf
  
  Possible precedence issue with control flow operator at /software/xxxx_pkgs/envs/ensemble-vep/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
  DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110) at /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/Bio/EnsEMBL/Registry.pm line 1771.
  
  -------------------- EXCEPTION --------------------
  MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110)
  STACK Bio::EnsEMBL::Registry::load_registry_from_db /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/Bio/EnsEMBL/Registry.pm:1771
  STACK Bio::EnsEMBL::VEP::BaseVEP::registry /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:163
  STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:80
  STACK Bio::EnsEMBL::VEP::Runner::init /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/modules/Bio/EnsEMBL/VEP/Runner.pm:72
  STACK Bio::EnsEMBL::VEP::Runner::run /software/xxxx_pkgs/envs/ensemble-vep/share/ensembl-vep-88.9-1/modules/Bio/EnsEMBL/VEP/Runner.pm:111
  STACK toplevel /software//envs/ensemble-vep/bin/vep:209
  Ensembl API version = 88
  ```
  
  ```
  
  **Tags:** vcf, sequence-annotation, ensembl, errors
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-11-12. Score: 2
  
  You might prefer to run [VEP](https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html) in offline mode:
  
  > Using `--cache` (without `--offline`) uses the local cache on disk to
  > fetch most annotations, but allows database connections for some
  > features (see [cache limitations](https://m.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations))
  
  If you need HGVS names in your output, you'll also need to supply a FASTA file using `--fasta`:
  
  > [--offline](https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_offline)
  >
  > Enable offline mode. No database connections will be made, and a cache file or GFF/GTF file is required for annotation. Add
  > --refseq to use the refseq cache (if installed). Not used by default.
  
  > [--fasta [file|dir]](https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_fasta)
  >
  > Specify a FASTA file or a directory containing FASTA files to use to look up reference sequence. The first time you run VEP with this parameter an index will be built which can take a few minutes. This is required if fetching HGVS annotations (--hgvs) or checking reference sequences (--check\_ref) in offline mode (--offline), and optional with some performance increase in cache mode (--cache). See documentation for more details. Not used by default.
  
  
  ---
  
  