[ensembl-dev] VEP options not working as described in documentation

[Wallace Ko]

Hi Ensembl Developers,

I have tested a number of options and observed behaviors that are
unexpected or not described in documentation. Below are the test cases with
examples, assuming VEP 99 installed in /opt/vep and cache installed in
/opt/vep/data:

   1. --verbose option does not enable output of config lines as described
   in documentation
   <https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_config>
   .

   *Test command. 1*:
   /opt/vep/vep --dir /opt/vep/data --cache --offline --no_stats
   --force_overwrite --json --output_file out -i test.vcf

   *STDOUT/STDERR 1*:
   2020-04-20 13:42:55 - Auto-detected FASTA file in cache directory
   WARNING: No input file format specified - detected vcf format

   *Output files 1*:
   * out

   2. --verbose enables output of warning messages to both STDERR and
   <output_file>_warnings.txt. If --warning_file STDERR is specified,
   duplicate warning messages are found in STDERR.

   *Test command 2.1*:
   /opt/vep/vep --dir /opt/vep/data --cache --offline --no_stats
   --force_overwrite --json --output_file out -i test.vcf --verbose

   *STDOUT/STDERR 2.1*:
   2020-04-20 13:44:43 - Auto-detected FASTA file in cache directory
   WARNING: No input file format specified - detected vcf format

   *Output files 2.1*:
   * out
   * out_warnings.txt


   *Test command 2.2*:
   /opt/vep/vep --dir /opt/vep/data --cache --offline --no_stats
   --force_overwrite --json --output_file out -i test.vcf --verbose
   --warning_file STDERR

   *STDOUT/STDERR 2.2*:
   2020-04-20 13:50:08 - Auto-detected FASTA file in cache directory
   WARNING: No input file format specified - detected vcf format
   WARNING: No input file format specified - detected vcf format

   *Output files 2.2*:
   * out

   3. --dir, --input_file, --output_file options do not work if specified
   in config file.

   *Test command 3.1*:
   /opt/vep/vep --config ./vep.ini

   *./vep.ini 3.1*:
   dir             /opt/vep/data
   verbose         1
   cache           1
   offline         1
   no_stats        1
   force_overwrite 1
   json            1
   input_file      test.vcf
   output_file     out
   warning_file    STDERR

   *STDOUT/STDERR 3.1*:

   -------------------- EXCEPTION --------------------
   MSG: ERROR: Cache directory /home/wallace/.vep/homo_sapiens not found

   STACK Bio::EnsEMBL::VEP::CacheDir::dir
   /opt/vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311
   STACK Bio::EnsEMBL::VEP::CacheDir::init
   /opt/vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227
   STACK Bio::EnsEMBL::VEP::CacheDir::new
   /opt/vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
   STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache
   /opt/vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115
   STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all
   /opt/vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91
   STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources
   /opt/vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175
   STACK Bio::EnsEMBL::VEP::Runner::init
   /opt/vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
   STACK Bio::EnsEMBL::VEP::Runner::run
   /opt/vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
   STACK toplevel /opt/vep/vep:224
   Date (localtime)    = Mon Apr 20 13:55:16 2020
   Ensembl API version = 99
   ---------------------------------------------------

   *Output files 3.1*: None


   *Test command 3.2*:
   /opt/vep/vep --dir /opt/vep/data

   */opt/vep/data/vep.ini 3.2*:
   verbose         1
   cache           1
   offline         1
   no_stats        1
   force_overwrite 1
   json            1
   input_file      test.vcf
   output_file     out
   warning_file    STDERR

   *STDOUT/STDERR 3.2*:
   2020-04-20 13:58:48 - Auto-detected FASTA file in cache directory
   Cannot detect format from STDIN - specify format with --format [format]
   at /opt/vep/modules/Bio/EnsEMBL/VEP/Parser.pm line 369.

   *Output files 3.2*: None


   *Test command 3.3*:
   /opt/vep/vep --dir /opt/vep/data -i test.vcf

   */opt/vep/data/vep.ini 3.3*:
   verbose         1
   cache           1
   offline         1
   no_stats        1
   force_overwrite 1
   json            1
   output_file     out
   warning_file    STDERR

   *STDOUT/STDERR 3.3*:
   2020-04-20 14:02:11 - Auto-detected FASTA file in cache directory
   WARNING: No input file format specified - detected vcf format
   WARNING: No input file format specified - detected vcf format

   *Output files 3.3*:
   * variant_effect_output.txt


   *Test command 3.4*:
   /opt/vep/vep --dir /opt/vep/data -i test.vcf -o out

   */opt/vep/data/vep.ini 3.4*:
   verbose         1
   cache           1
   offline         1
   no_stats        1
   force_overwrite 1
   json            1
   warning_file    STDERR

   *STDOUT/STDERR 3.4*:
   2020-04-20 14:02:11 - Auto-detected FASTA file in cache directory
   WARNING: No input file format specified - detected vcf format
   WARNING: No input file format specified - detected vcf format

   *Output files 3.4*:
   * out

   4. Log message are gone if output file is STDOUT:

   *Test command 4*:
   /opt/vep/vep --dir /opt/vep/data -i test.vcf -o STDOUT

   *./vep.ini 4*:
   verbose         1
   cache           1
   offline         1
   no_stats        1
   force_overwrite 1
   json            1
   warning_file    STDERR

   *STDOUT/STDERR 4*:
   {"allele_string":...}

   *Output files 4*: None

Case 2.2 and 4 seem like unwanted behaviors to me.
Anyway, if these are expected per design, it would be great to be
documented.

Thank you.

Regards,
Wallace Ko
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