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<p>Dear devs,</p>
<p>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.</p>
<p><i>WARNING: Plugin 'NearestGene' went wrong: ERROR: Could not get
gene adaptor; this plugin does not work in --offline mode</i></p>
<p>There's an issue with gene adaptor code,<b> $self->{ga} ||=
$self->{config}->{ga}</b>. Trying to guess where did {ga}
gone printing Dump of $self->{config} but I can't figure this
out:</p>
<p>$VAR1 = {<br>
'buffer_size' => 5000,<br>
'af_1kg' => 1,<br>
'species' => 'homo_sapiens',<br>
'stats_html' => 1,<br>
'host' => 'sake',<br>
'format' => 'vcf',<br>
'reg' => 'Bio::EnsEMBL::Registry',<br>
'chunk_size' => 50000,<br>
'check_existing' => 1,<br>
'freq_pop' => '1KG_ALL',<br>
'custom' => [],<br>
'cell_type' => [],<br>
'input_file' => 'test.vcf',<br>
'tmpdir' => '/tmp',<br>
'freq_filter' => 'exclude',<br>
'user' => 'bioinfo',<br>
'phastCons' => [],<br>
'terms' => 'SO',<br>
'delimiter' => ' ',<br>
'dir_cache' => '/home/gmarco/.vep',<br>
'polyphen_analysis' => 'humvar',<br>
'cache' => 1,<br>
'port' => '3306',<br>
'plugin' => [<br>
'Test'<br>
],<br>
'freq_gt_lt' => 'gt',<br>
'output_format' => 'vcf',<br>
'phyloP' => [],<br>
'numbers' => 1,<br>
'af_exac' => 1,<br>
'output_file' => '/tmp/test_88.vcf',<br>
'database' => 0,<br>
'freq_freq' => '0.01',<br>
'dir_plugins' =>
'/home/gmarco/repositories/vep_ensembl/Plugins',<br>
'core_type' => 'core',<br>
'vcf' => 1,<br>
'assembly' => 'GRCh38',<br>
'af' => 1,<br>
'terminal_width' => 48,<br>
'vcf_info_field' => 'CSQ',<br>
'transcript_filter' => [],<br>
'af_esp' => 1,<br>
'pick_order' => [<br>
'canonical',<br>
'appris',<br>
'tsl',<br>
'biotype',<br>
'ccds',<br>
'rank',<br>
'length',<br>
'ensembl',<br>
'refseq'<br>
],<br>
'biotype' => 1,<br>
'cache_region_size' => 1000000,<br>
'symbol' => 1,<br>
'ucsc_data_root' =>
'<a class="moz-txt-link-freetext" href="http://hgdownload.cse.ucsc.edu/goldenpath/">http://hgdownload.cse.ucsc.edu/goldenpath/</a>',<br>
'synonyms' =>
'/home/gmarco/.vep/homo_sapiens/88_GRCh38/chr_synonyms.txt',<br>
'dir' => '/home/gmarco/.vep',<br>
'password' => 'A29bcd1234#',<br>
'no_slice_cache' => 1,<br>
'failed' => 0,<br>
'force_overwrite' => 1,<br>
'fasta' =>
'/home/gmarco/.vep/homo_sapiens/88_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz'<br>
};</p>
<p>Regards,<br>
Guillermo<br>
</p>
<p><br>
<br>
</p>
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