<div dir="ltr">Hi Nicolas,<div><br></div><div>Thanks for reporting this, it has now been fixed on the release/80 branch of ensembl-variation.</div><div><br></div><div>You can re-run INSTALL.pl to get the fix if that's what you used initially, or run "git pull" in your ensembl-variation directory if you used Git to set up your API installation.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 18 June 2015 at 11:50, Nicolas Thierry-Mieg <span dir="ltr"><<a href="mailto:Nicolas.Thierry-Mieg@imag.fr" target="_blank">Nicolas.Thierry-Mieg@imag.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear developers,<br>
<br>
we use VEP with custom annotations (in a targeted sequencing project).<br>
The following test was working fine with VEP v76, but now fails with the latest v80.<br>
<br>
The test is performed in a clean subdir.<br>
The computer is running Centos6 x86_64 fully up-to-date.<br>
<br>
The test files are as follows:<br>
<br>
[nthierry@timc-bcm-07 Test_VEP_80]$ cat transcript_reorder.gff<br>
3 protein_coding exon 113077591 113077946 . - . gene_id toto; transcript_id toto_a; exon_number 1;<br>
3 protein_coding CDS 113077591 113077746 . - 0 gene_id toto; transcript_id toto_a; product_id toto_a; exon_number 1;<br>
3 protein_coding start_codon 113077744 113077746 . - . gene_id toto; transcript_id toto_a; product_id toto_a;<br>
3 protein_coding exon 113063155 113063561 . - . gene_id toto; transcript_id toto_a; exon_number 2;<br>
3 protein_coding stop_codon 113063352 113063354 . - . gene_id toto; transcript_id toto_a; product_id toto_a;<br>
3 protein_coding CDS 113063355 113063561 . - 0 gene_id toto; transcript_id toto_a; product_id toto_a; exon_number 2;<br>
[nthierry@timc-bcm-07 Test_VEP_80]$<br>
<br>
[nthierry@timc-bcm-07 Test_VEP_80]$ cat snp.vcf<br>
#CHROM POS ID REF ALT QUAL FILTER INFO<br>
3 113063450 . G A . PASS<br>
[nthierry@timc-bcm-07 Test_VEP_80]$<br>
<br>
<br>
[nthierry@timc-bcm-07 Test_VEP_80]$ perl <a href="http://gtf2vep.pl" rel="noreferrer" target="_blank">gtf2vep.pl</a> -i transcript_reorder.gff -f hs.chrom_3.fasta --dir cache/ -d 1 -s homo_sapiens<br>
2015-06-18 12:26:23 - Checking/creating FASTA index<br>
2015-06-18 12:26:23 - Processing chromosome 3<br>
2015-06-18 12:26:23 - All done!<br>
<br>
[This seems to work, cache/ now contains a single file: cache/homo_sapiens/1/3/113000001-114000000.gz ]<br>
<br>
<br>
[nthierry@timc-bcm-07 Test_VEP_80]$ perl <a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a> --offline -i snp.vcf --vcf --dir_cache cache/ --cache_version 1 --force --no_stats<br>
2015-06-18 12:26:29 - Starting...<br>
<br>
-------------------- EXCEPTION --------------------<br>
MSG: Can not find internal name for species 'homo_sapiens'<br>
STACK Bio::EnsEMBL::Registry::get_adaptor /home/nthierry/Test_VEP_80/Bio/EnsEMBL/Registry.pm:985<br>
STACK Bio::EnsEMBL::Variation::Utils::VEP::get_version_data /home/nthierry/Test_VEP_80/Bio/EnsEMBL/Variation/Utils/VEP.pm:6120<br>
STACK main::get_out_file_handle <a href="http://variant_effect_predictor.pl:1862" rel="noreferrer" target="_blank">variant_effect_predictor.pl:1862</a><br>
STACK main::main <a href="http://variant_effect_predictor.pl:227" rel="noreferrer" target="_blank">variant_effect_predictor.pl:227</a><br>
STACK toplevel <a href="http://variant_effect_predictor.pl:145" rel="noreferrer" target="_blank">variant_effect_predictor.pl:145</a><br>
Date (localtime) = Thu Jun 18 12:26:29 2015<br>
Ensembl API version = 80<br>
---------------------------------------------------<br>
<br>
<br>
<br>
The same test when using VEP v76 worked well:<br>
<br>
[nthierry@timc-bcm-07 Test_VEP_76]$ perl <a href="http://gtf2vep.pl" rel="noreferrer" target="_blank">gtf2vep.pl</a> -i transcript_reorder.gff -f hs.chrom_3.fasta --dir cache/ -d 1 -s homo_sapiens<br>
2015-06-18 12:45:50 - Checking/creating FASTA index<br>
2015-06-18 12:45:50 - Processing chromosome 3<br>
2015-06-18 12:45:50 - All done!<br>
[nthierry@timc-bcm-07 Test_VEP_76]$ perl <a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a> --offline -i snp.vcf --vcf --dir_cache cache/ --cache_version 1 --force --no_stats<br>
2015-06-18 12:45:55 - Starting...<br>
2015-06-18 12:45:55 - Detected format of input file as vcf<br>
2015-06-18 12:45:55 - Read 1 variants into buffer<br>
2015-06-18 12:45:55 - Reading transcript data from cache and/or database<br>
[===============================================] [ 100% ]<br>
2015-06-18 12:45:55 - Retrieved 1 transcripts (0 mem, 1 cached, 0 DB, 0 duplicates)<br>
2015-06-18 12:45:55 - Analyzing chromosome 3<br>
2015-06-18 12:45:55 - Analyzing variants<br>
[===============================================] [ 100% ]<br>
2015-06-18 12:45:55 - Calculating consequences<br>
2015-06-18 12:45:55 - Processed 1 total variants (1 vars/sec, 1 vars/sec total)<br>
2015-06-18 12:45:55 - Finished!<br>
[nthierry@timc-bcm-07 Test_VEP_76]$<br>
<br>
<br>
Any ideas?<br>
<br>
Regards,<br>
Nicolas<br>
<br>
<br>
-- <br>
------------------------------------------------------------<br>
Nicolas Thierry-Mieg<br>
Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525<br>
Pavillon Taillefer, Faculte de Medecine<br>
38706 La Tronche cedex, France<br>
tel: <a href="tel:%28%2B33%29456.520.067" value="+33456520067" target="_blank">(+33)456.520.067</a>, fax: <a href="tel:%28%2B33%29456.520.055" value="+33456520055" target="_blank">(+33)456.520.055</a><br>
------------------------------------------------------------<br>
<br>
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</blockquote></div><br></div>