<div dir="ltr">No, the script version should match the API/DB version - perhaps at some point 80 is getting inserted instead of 82?<div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 2 October 2015 at 00:12, 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 Will,<br>
<br>
Updating the API installation did help, no more noisy warning messages. Thanks<br>
you!<br>
<br>
One more question. After the upgrade, is this normal:<br>
<br>
$ <a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a><br>
#----------------------------------#<br>
# ENSEMBL VARIANT EFFECT PREDICTOR #<br>
#----------------------------------#<br>
<br>
version 80<br>
by Will McLaren (<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)<br>
<br>
Help: <a href="mailto:dev@ensembl.org">dev@ensembl.org</a> , <a href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a><br>
Twitter: @ensembl , @EnsemblWill<br>
<...><br>
<br>
Note the script version which does not match the API/database one.<br>
<br>
Thanks,<br>
Ivan<br>
<div class="HOEnZb"><div class="h5"><br>
On Thursday, October 01, 2015 11:01:35 AM Will McLaren wrote:<br>
> Hi Ivan<br>
><br>
> Thanks for the report. We have a data bug in the GRCh37 VEP cache that<br>
> means some protein domain descriptions are incomplete.<br>
><br>
> I've added a fix to the VEP code to suppress the warning you are seeing<br>
> (re-run INSTALL.pl to pick it up); it may be that we are able to update the<br>
> cache at a later date with the missing data.<br>
><br>
> Regards<br>
><br>
> Will McLaren<br>
> Ensembl Variation<br>
><br>
> On 30 September 2015 at 23:41, Ivan Adzhubey <<a href="mailto:iadzhubey@rics.bwh.harvard.edu">iadzhubey@rics.bwh.harvard.edu</a><br>
> > wrote:<br>
> ><br>
> > Hi,<br>
> ><br>
> > $ <a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a> --offline --cache --assembly GRCh37<br>
> > --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<br>
> > 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>
> ><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<br>
> > > been<br>
> > > 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>
> > ><br>
> > > Highlights of this release include:<br>
> > ><br>
> > > Ensembl mobile website <<a href="http://m.ensembl.org/" rel="noreferrer" target="_blank">http://m.ensembl.org/</a>><br>
> > > Support of VEP Plugins through the web interface, script and REST<br>
> > > Improved Variation tables<br>
> > > <<br>
> ><br>
> > <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>
> ><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>
> > > 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>
> > > Exome Aggregation Consortium (ExAC <<a href="http://exac.broadinstitute.org/" rel="noreferrer" target="_blank">http://exac.broadinstitute.org/</a>>)<br>
> ><br>
> > Mouse<br>
> ><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>
> > > 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>
> > > <<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>
> > ><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>
> > > <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>
> > ><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>
> > > <<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>
</div></div><div class="HOEnZb"><div class="h5">_______________________________________________<br>
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</div></div></blockquote></div><br></div>