<div dir="ltr">Hi Ivan<div><br></div><div>Thanks for the report. We have a data bug in the GRCh37 VEP cache that means some protein domain descriptions are incomplete.</div><div><br></div><div>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.</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 30 September 2015 at 23:41, Ivan Adzhubey <span dir="ltr"><<a href="mailto:iadzhubey@rics.bwh.harvard.edu" target="_blank">iadzhubey@rics.bwh.harvard.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
$ <a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a> --offline --cache --assembly GRCh37 --format vcf -i<br>
example_GRCh37.vcf --everything -o example_annotated_GRCh37.vcf<br>
<br>
2015-09-30 17:39:59 - Read existing cache info<br>
2015-09-30 17:39:59 - INFO: Disabling --hgvs; using --offline and no FASTA file<br>
found<br>
2015-09-30 17:39:59 - Starting...<br>
2015-09-30 17:39:59 - Read 173 variants into buffer<br>
2015-09-30 17:39:59 - Checking for existing variations<br>
<...><br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
[============================><br>
]   [ 23% ]Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
Use of uninitialized value in concatenation (.) or string at<br>
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.<br>
<...><br>
<span class=""><br>
On Wednesday, September 30, 2015 01:41:00 PM Thomas Maurel wrote:<br>
> We are pleased to announce that the latest Ensembl update (e!82) has been<br>
</span>> released: <a href="http://www.ensembl.org/" rel="noreferrer" target="_blank">http://www.ensembl.org/</a> <<a href="http://www.ensembl.org/" rel="noreferrer" target="_blank">http://www.ensembl.org/</a>><br>
<span class="">><br>
> Highlights of this release include:<br>
><br>
</span>> Ensembl mobile website <<a href="http://m.ensembl.org/" rel="noreferrer" target="_blank">http://m.ensembl.org/</a>><br>
<span class="">> Support of VEP Plugins through the web interface, script and REST<br>
> Improved Variation tables<br>
</span>> <<a href="http://e82.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?g=ENSG000001" rel="noreferrer" target="_blank">http://e82.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?g=ENSG000001</a><br>
> 39618;r=13:32315474-32400266> RNASeq data set of Zebrafish<br>
> <<a href="http://e82.ensembl.org/Danio_rerio/Info/Index" rel="noreferrer" target="_blank">http://e82.ensembl.org/Danio_rerio/Info/Index</a>> developmental stages<br>
<span class="">> Marking a region on images<br>
> LastZ replaced TBlat for pairwise alignments<br>
> Human variation data updates to dbSNP (144) including variants from the<br>
</span>> Exome Aggregation Consortium (ExAC <<a href="http://exac.broadinstitute.org/" rel="noreferrer" target="_blank">http://exac.broadinstitute.org/</a>>) Mouse<br>
> <<a href="http://e82.ensembl.org/Mus_musculus/Info/Index" rel="noreferrer" target="_blank">http://e82.ensembl.org/Mus_musculus/Info/Index</a>>: updated to GENCODE M7<br>
<span class="">> including HAVANA annotation. Improved data upload form<br>
> Improvements to PDF export<br>
> Export mode for projectors and print<br>
> Phenotype data updated for several species, including human<br>
</span>> <<a href="http://e82.ensembl.org/Homo_sapiens/Phenotype/Locations?ph=5815" rel="noreferrer" target="_blank">http://e82.ensembl.org/Homo_sapiens/Phenotype/Locations?ph=5815</a>>, mouse<br>
> <<a href="http://e82.ensembl.org/Mus_musculus/Phenotype/Locations?ph=225" rel="noreferrer" target="_blank">http://e82.ensembl.org/Mus_musculus/Phenotype/Locations?ph=225</a>>, rat<br>
> <<a href="http://e82.ensembl.org/Rattus_norvegicus/Phenotype/Locations?ph=73" rel="noreferrer" target="_blank">http://e82.ensembl.org/Rattus_norvegicus/Phenotype/Locations?ph=73</a>> and<br>
> horse <<a href="http://e82.ensembl.org/Equus_caballus/Info/Index" rel="noreferrer" target="_blank">http://e82.ensembl.org/Equus_caballus/Info/Index</a>><br>
<span class="">><br>
> A complete list of the changes in release 82 can be found at<br>
> <a href="http://www.ensembl.org/info/website/news.html" rel="noreferrer" target="_blank">http://www.ensembl.org/info/website/news.html</a><br>
> <<a href="http://www.ensembl.org/info/website/news.html" rel="noreferrer" target="_blank">http://www.ensembl.org/info/website/news.html</a>><br>
><br>
> For the latest news from the Ensembl project visit our blog at<br>
</span>> <a href="http://www.ensembl.info" rel="noreferrer" target="_blank">http://www.ensembl.info</a> <<a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a>><br>
<span class="">><br>
> The release 82 blog post can be viewed here:<br>
> <a href="http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/" rel="noreferrer" target="_blank">http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/</a><br>
> <<a href="http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/" rel="noreferrer" target="_blank">http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/</a>><br>
><br>
> The e82 webinar is planned for Wednesday 7th Oct at 16:00 GMT+1, please<br>
> register using the following URL (registration is free):<br>
> <a href="http://www.ebi.ac.uk/training/events/2015/ensembl-release-82-webinar" rel="noreferrer" target="_blank">http://www.ebi.ac.uk/training/events/2015/ensembl-release-82-webinar</a><br>
</span>> <<a href="https://attendee.gototraining.com/r/1571390501370151169" rel="noreferrer" target="_blank">https://attendee.gototraining.com/r/1571390501370151169</a>><br>
><br>
><br>
> Best Regards,<br>
> Thomas<br>
<br>
<br>
--<br>
Ivan Adzhubey, Ph.D.<br>
Instructor<br>
Division of Genetics, Dept of Medicine<br>
Brigham & Women's Hospital<br>
Harvard Medical School<br>
New Research Building, Room 0464C<br>
77 Avenue Louis Pasteur<br>
Boston, MA 02115<br>
tel.: <a href="tel:%28617%29%20525-4728" value="+16175254728">(617) 525-4728</a><br>
fax:  <a href="tel:%28617%29%20525-4705" value="+16175254705">(617) 525-4705</a><br>
web: <a href="http://genetics.bwh.harvard.edu/wiki/sunyaevlab/" rel="noreferrer" target="_blank">http://genetics.bwh.harvard.edu/wiki/sunyaevlab/</a><br>
<br>
<br>
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</blockquote></div><br></div>