[ensembl-dev] problem with VEP v80 - regression

Will McLaren wm2 at ebi.ac.uk
Thu Jun 18 11:59:59 BST 2015


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
> 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 -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
> --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
> STACK main::main variant_effect_predictor.pl:227
> STACK toplevel 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 -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
> --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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