[ensembl-dev] problem with VEP v80 - regression
Nicolas Thierry-Mieg
Nicolas.Thierry-Mieg at imag.fr
Thu Jun 18 12:11:00 BST 2015
Confirmed fixed for me (yes I had used INSTALL.pl, I re-ran that script
to update).
Thanks for a lightning-fast fix!
On 06/18/2015 12:59 PM, Will McLaren wrote:
> Hi Nicolas,
>
> Thanks for reporting this, it has now been fixed on the release/80
> branch of ensembl-variation.
>
> 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.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 18 June 2015 at 11:50, Nicolas Thierry-Mieg
> <Nicolas.Thierry-Mieg at imag.fr <mailto:Nicolas.Thierry-Mieg at imag.fr>> wrote:
>
> Dear developers,
>
> we use VEP with custom annotations (in a targeted sequencing project).
> The following test was working fine with VEP v76, but now fails with
> the latest v80.
>
> The test is performed in a clean subdir.
> The computer is running Centos6 x86_64 fully up-to-date.
>
> The test files are as follows:
>
> [nthierry at timc-bcm-07 Test_VEP_80]$ cat transcript_reorder.gff
> 3 protein_coding exon 113077591 113077946 .
> - . gene_id toto; transcript_id toto_a; exon_number 1;
> 3 protein_coding CDS 113077591 113077746 .
> - 0 gene_id toto; transcript_id toto_a; product_id
> toto_a; exon_number 1;
> 3 protein_coding start_codon 113077744 113077746
> . - . gene_id toto; transcript_id toto_a;
> product_id toto_a;
> 3 protein_coding exon 113063155 113063561 .
> - . gene_id toto; transcript_id toto_a; exon_number 2;
> 3 protein_coding stop_codon 113063352 113063354
> . - . gene_id toto; transcript_id toto_a;
> product_id toto_a;
> 3 protein_coding CDS 113063355 113063561 .
> - 0 gene_id toto; transcript_id toto_a; product_id
> toto_a; exon_number 2;
> [nthierry at timc-bcm-07 Test_VEP_80]$
>
> [nthierry at timc-bcm-07 Test_VEP_80]$ cat snp.vcf
> #CHROM POS ID REF ALT QUAL FILTER INFO
> 3 113063450 . G A . PASS
> [nthierry at timc-bcm-07 Test_VEP_80]$
>
>
> [nthierry at timc-bcm-07 Test_VEP_80]$ perl gtf2vep.pl
> <http://gtf2vep.pl> -i transcript_reorder.gff -f hs.chrom_3.fasta
> --dir cache/ -d 1 -s homo_sapiens
> 2015-06-18 12:26:23 - Checking/creating FASTA index
> 2015-06-18 12:26:23 - Processing chromosome 3
> 2015-06-18 12:26:23 - All done!
>
> [This seems to work, cache/ now contains a single file:
> cache/homo_sapiens/1/3/113000001-114000000.gz ]
>
>
> [nthierry at timc-bcm-07 Test_VEP_80]$ perl variant_effect_predictor.pl
> <http://variant_effect_predictor.pl> --offline -i snp.vcf --vcf
> --dir_cache cache/ --cache_version 1 --force --no_stats
> 2015-06-18 12:26:29 - Starting...
>
> -------------------- EXCEPTION --------------------
> MSG: Can not find internal name for species 'homo_sapiens'
> STACK Bio::EnsEMBL::Registry::get_adaptor
> /home/nthierry/Test_VEP_80/Bio/EnsEMBL/Registry.pm:985
> STACK Bio::EnsEMBL::Variation::Utils::VEP::get_version_data
> /home/nthierry/Test_VEP_80/Bio/EnsEMBL/Variation/Utils/VEP.pm:6120
> STACK main::get_out_file_handle variant_effect_predictor.pl:1862
> <http://variant_effect_predictor.pl:1862>
> STACK main::main variant_effect_predictor.pl:227
> <http://variant_effect_predictor.pl:227>
> STACK toplevel variant_effect_predictor.pl:145
> <http://variant_effect_predictor.pl:145>
> Date (localtime) = Thu Jun 18 12:26:29 2015
> Ensembl API version = 80
> ---------------------------------------------------
>
>
>
> The same test when using VEP v76 worked well:
>
> [nthierry at timc-bcm-07 Test_VEP_76]$ perl gtf2vep.pl
> <http://gtf2vep.pl> -i transcript_reorder.gff -f hs.chrom_3.fasta
> --dir cache/ -d 1 -s homo_sapiens
> 2015-06-18 12:45:50 - Checking/creating FASTA index
> 2015-06-18 12:45:50 - Processing chromosome 3
> 2015-06-18 12:45:50 - All done!
> [nthierry at timc-bcm-07 Test_VEP_76]$ perl variant_effect_predictor.pl
> <http://variant_effect_predictor.pl> --offline -i snp.vcf --vcf
> --dir_cache cache/ --cache_version 1 --force --no_stats
> 2015-06-18 12:45:55 - Starting...
> 2015-06-18 12:45:55 - Detected format of input file as vcf
> 2015-06-18 12:45:55 - Read 1 variants into buffer
> 2015-06-18 12:45:55 - Reading transcript data from cache and/or database
> [===============================================] [ 100% ]
> 2015-06-18 12:45:55 - Retrieved 1 transcripts (0 mem, 1 cached, 0
> DB, 0 duplicates)
> 2015-06-18 12:45:55 - Analyzing chromosome 3
> 2015-06-18 12:45:55 - Analyzing variants
> [===============================================] [ 100% ]
> 2015-06-18 12:45:55 - Calculating consequences
> 2015-06-18 12:45:55 - Processed 1 total variants (1 vars/sec, 1
> vars/sec total)
> 2015-06-18 12:45:55 - Finished!
> [nthierry at timc-bcm-07 Test_VEP_76]$
>
>
> Any ideas?
>
> Regards,
> Nicolas
>
>
--
------------------------------------------------------------
Nicolas Thierry-Mieg
Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525
Pavillon Taillefer, Faculte de Medecine
38706 La Tronche cedex, France
tel: (+33)456.520.067, fax: (+33)456.520.055
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