[ensembl-dev] Ensembl release 82 is out!

Will McLaren wm2 at ebi.ac.uk
Thu Oct 1 10:01:35 BST 2015


Hi Ivan

Thanks for the report. We have a data bug in the GRCh37 VEP cache that
means some protein domain descriptions are incomplete.

I've added a fix to the VEP code to suppress the warning you are seeing
(re-run INSTALL.pl to pick it up); it may be that we are able to update the
cache at a later date with the missing data.

Regards

Will McLaren
Ensembl Variation

On 30 September 2015 at 23:41, Ivan Adzhubey <iadzhubey at rics.bwh.harvard.edu
> wrote:

> Hi,
>
> $ variant_effect_predictor.pl --offline --cache --assembly GRCh37
> --format vcf -i
> example_GRCh37.vcf --everything -o example_annotated_GRCh37.vcf
>
> 2015-09-30 17:39:59 - Read existing cache info
> 2015-09-30 17:39:59 - INFO: Disabling --hgvs; using --offline and no FASTA
> file
> found
> 2015-09-30 17:39:59 - Starting...
> 2015-09-30 17:39:59 - Read 173 variants into buffer
> 2015-09-30 17:39:59 - Checking for existing variations
> <...>
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> [============================>
> ]   [ 23% ]Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> Use of uninitialized value in concatenation (.) or string at
> /net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
> <...>
>
> On Wednesday, September 30, 2015 01:41:00 PM Thomas Maurel wrote:
> > We are pleased to announce that the latest Ensembl update (e!82) has been
> > released: http://www.ensembl.org/ <http://www.ensembl.org/>
> >
> > Highlights of this release include:
> >
> > Ensembl mobile website <http://m.ensembl.org/>
> > Support of VEP Plugins through the web interface, script and REST
> > Improved Variation tables
> > <
> http://e82.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?g=ENSG000001
> > 39618;r=13:32315474-32400266> RNASeq data set of Zebrafish
> > <http://e82.ensembl.org/Danio_rerio/Info/Index> developmental stages
> > Marking a region on images
> > LastZ replaced TBlat for pairwise alignments
> > Human variation data updates to dbSNP (144) including variants from the
> > Exome Aggregation Consortium (ExAC <http://exac.broadinstitute.org/>)
> Mouse
> > <http://e82.ensembl.org/Mus_musculus/Info/Index>: updated to GENCODE M7
> > including HAVANA annotation. Improved data upload form
> > Improvements to PDF export
> > Export mode for projectors and print
> > Phenotype data updated for several species, including human
> > <http://e82.ensembl.org/Homo_sapiens/Phenotype/Locations?ph=5815>, mouse
> > <http://e82.ensembl.org/Mus_musculus/Phenotype/Locations?ph=225>, rat
> > <http://e82.ensembl.org/Rattus_norvegicus/Phenotype/Locations?ph=73> and
> > horse <http://e82.ensembl.org/Equus_caballus/Info/Index>
> >
> > A complete list of the changes in release 82 can be found at
> > http://www.ensembl.org/info/website/news.html
> > <http://www.ensembl.org/info/website/news.html>
> >
> > For the latest news from the Ensembl project visit our blog at
> > http://www.ensembl.info <http://www.ensembl.info/>
> >
> > The release 82 blog post can be viewed here:
> > http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/
> > <http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/>
> >
> > The e82 webinar is planned for Wednesday 7th Oct at 16:00 GMT+1, please
> > register using the following URL (registration is free):
> > http://www.ebi.ac.uk/training/events/2015/ensembl-release-82-webinar
> > <https://attendee.gototraining.com/r/1571390501370151169>
> >
> >
> > Best Regards,
> > Thomas
>
>
> --
> Ivan Adzhubey, Ph.D.
> Instructor
> Division of Genetics, Dept of Medicine
> Brigham & Women's Hospital
> Harvard Medical School
> New Research Building, Room 0464C
> 77 Avenue Louis Pasteur
> Boston, MA 02115
> tel.: (617) 525-4728
> fax:  (617) 525-4705
> web: http://genetics.bwh.harvard.edu/wiki/sunyaevlab/
>
>
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