[ensembl-dev] VEP: Plugin problems with gene adaptor

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Mon May 15 08:44:24 BST 2017


Dear devs,

I've recently updated to Ensembl VEP 88 and I'm facing some problems 
with some plugins. Trying to run NearestGene.pm plugin and I can't make 
it run.

/WARNING: Plugin 'NearestGene' went wrong: ERROR: Could not get gene 
adaptor; this plugin does not work in --offline mode/

There's an issue with gene adaptor code,*$self->{ga} ||= 
$self->{config}->{ga}*. Trying to guess where did {ga} gone printing 
Dump of $self->{config} but I can't figure this out:

$VAR1 = {
   'buffer_size' => 5000,
   'af_1kg' => 1,
   'species' => 'homo_sapiens',
   'stats_html' => 1,
   'host' => 'sake',
   'format' => 'vcf',
   'reg' => 'Bio::EnsEMBL::Registry',
   'chunk_size' => 50000,
   'check_existing' => 1,
   'freq_pop' => '1KG_ALL',
   'custom' => [],
   'cell_type' => [],
   'input_file' => 'test.vcf',
   'tmpdir' => '/tmp',
   'freq_filter' => 'exclude',
   'user' => 'bioinfo',
   'phastCons' => [],
   'terms' => 'SO',
   'delimiter' => '    ',
   'dir_cache' => '/home/gmarco/.vep',
   'polyphen_analysis' => 'humvar',
   'cache' => 1,
   'port' => '3306',
   'plugin' => [
     'Test'
   ],
   'freq_gt_lt' => 'gt',
   'output_format' => 'vcf',
   'phyloP' => [],
   'numbers' => 1,
   'af_exac' => 1,
   'output_file' => '/tmp/test_88.vcf',
   'database' => 0,
   'freq_freq' => '0.01',
   'dir_plugins' => '/home/gmarco/repositories/vep_ensembl/Plugins',
   'core_type' => 'core',
   'vcf' => 1,
   'assembly' => 'GRCh38',
   'af' => 1,
   'terminal_width' => 48,
   'vcf_info_field' => 'CSQ',
   'transcript_filter' => [],
   'af_esp' => 1,
   'pick_order' => [
     'canonical',
     'appris',
     'tsl',
     'biotype',
     'ccds',
     'rank',
     'length',
     'ensembl',
     'refseq'
   ],
   'biotype' => 1,
   'cache_region_size' => 1000000,
   'symbol' => 1,
   'ucsc_data_root' => 'http://hgdownload.cse.ucsc.edu/goldenpath/',
   'synonyms' => 
'/home/gmarco/.vep/homo_sapiens/88_GRCh38/chr_synonyms.txt',
   'dir' => '/home/gmarco/.vep',
   'password' => 'A29bcd1234#',
   'no_slice_cache' => 1,
   'failed' => 0,
   'force_overwrite' => 1,
   'fasta' => 
'/home/gmarco/.vep/homo_sapiens/88_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz'
};

Regards,
Guillermo



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