[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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