<table cellspacing="0" cellpadding="0" border="0"><tr><td valign="top">Hi!<div id="yMail_cursorElementTracker_0.9143827212974429">I would like to notify you that dating sites are using this site to post advertisements......i received two ads this morning. ..!</div><div id="yMail_cursorElementTracker_0.9143827212974429">Thanks! <br><br><p><a href="https://overview.mail.yahoo.com/mobile/?.src=Android">Sent from Yahoo Mail on Android</a></p> <hr><table cellspacing="0" cellpadding="0" border="0"> <tbody> <tr> <td valign="top"> <div style="font-family:Roboto, sans-serif;color:#7e7d80;"><b>From</b>:"Will McLaren" <wm2@ebi.ac.uk><br><b>Date</b>:Mon, 27 Jul, 2015 at 13:27<br><b>Subject</b>:Re: [ensembl-dev] VEP unable to connect to Ensembl Genomes<br><br></div> <div dir="ltr">Hi Nikolas,<div><br clear="none"></div><div>The VEP INSTALL.pl script offers an update option, simply run:</div><div><br clear="none"></div><div>perl INSTALL.pl
--UPDATE</div><div><br clear="none"></div><div>Regards</div><div><br clear="none"></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="yQTDBase yqt5718999507" id="yqt88611"><div class="gmail_extra"><br clear="none"><div class="gmail_quote">On 25 July 2015 at 11:45, Nikolas Pontikos <span dir="ltr"><<a rel="nofollow" shape="rect" ymailto="mailto:n.pontikos@ucl.ac.uk" target="_blank" href="javascript:return">n.pontikos@ucl.ac.uk</a>></span> wrote:<br clear="none"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello Magali,<br clear="none">
<br clear="none">
There is no particular reason except that I haven't gotten round to<br clear="none">
updating our installation.<br clear="none">
Incidentally, what is the most straightforward way of doing an update?<br clear="none">
<br clear="none">
Thanks,<br clear="none">
<br clear="none">
Nikolas.<br clear="none">
<div class="HOEnZb"><div class="h5"><br clear="none">
<br clear="none">
On 17 July 2015 at 11:33, mag <<a rel="nofollow" shape="rect" ymailto="mailto:mr6@ebi.ac.uk" target="_blank" href="javascript:return">mr6@ebi.ac.uk</a>> wrote:<br clear="none">
> Hi Nikolas,<br clear="none">
><br clear="none">
> Apologies for the misleading information, we officially support 2 releases<br clear="none">
> at one given time, the current one and the previous one<br clear="none">
> <a rel="nofollow" shape="rect" target="_blank" href="http://grch37.ensembl.org/info/data/mysql.html">http://grch37.ensembl.org/info/data/mysql.html</a><br clear="none">
><br clear="none">
> The release 79 databases have not yet been cleared up following release 81,<br clear="none">
> but we cannot guarantee they will remain available much longer, as this<br clear="none">
> depends on the space available on the server.<br clear="none">
><br clear="none">
> May I ask if there is a particular reason you are using version 78 and not a<br clear="none">
> more recent one?<br clear="none">
><br clear="none">
><br clear="none">
> Regards,<br clear="none">
> Magali<br clear="none">
><br clear="none">
><br clear="none">
> On 17/07/2015 10:56, mag wrote:<br clear="none">
>><br clear="none">
>> Hi Nikolas,<br clear="none">
>><br clear="none">
>> We are currently maintaining 3 releases worth of databases on the<br clear="none">
>> dedicated GRCh37 MySQL server.<br clear="none">
>> As 81 was released yesterday, 78 has now been removed.<br clear="none">
>> You can still access releases 79, 80 and 81 for the GRCh37 assembly.<br clear="none">
>><br clear="none">
>><br clear="none">
>> Hope this helps,<br clear="none">
>> Magali<br clear="none">
>><br clear="none">
>> On 17/07/2015 10:46, Nikolas Pontikos wrote:<br clear="none">
>>><br clear="none">
>>> Yes I've just witnessed the same problem.<br clear="none">
>>> Code used to work, nothing changed and stopped working.<br clear="none">
>>> Something might have changed on the server side.<br clear="none">
>>> Adding the --offline flag seems to have fixed it.<br clear="none">
>>> This is the error message below:<br clear="none">
>>><br clear="none">
>>><br clear="none">
>>> #----------------------------------#<br clear="none">
>>> # ENSEMBL VARIANT EFFECT PREDICTOR #<br clear="none">
>>> #----------------------------------#<br clear="none">
>>><br clear="none">
>>> version 78<br clear="none">
>>><br clear="none">
>>> By Will McLaren (<a rel="nofollow" shape="rect" ymailto="mailto:wm2@ebi.ac.uk" target="_blank" href="javascript:return">wm2@ebi.ac.uk</a>)<br clear="none">
>>><br clear="none">
>>> Configuration options:<br clear="none">
>>><br clear="none">
>>> assembly GRCh37<br clear="none">
>>> canonical 1<br clear="none">
>>> check_alleles 1<br clear="none">
>>> check_existing 1<br clear="none">
>>> core_type core<br clear="none">
>>> database 1<br clear="none">
>>> dir /home/rmhanpo/.vep<br clear="none">
>>> dir_plugins /home/rmhanpo/.vep/Plugins<br clear="none">
>>> fasta<br clear="none">
>>><br clear="none">
>>> /scratch2/vyp-scratch2/reference_datasets/human_reference_sequence/human_g1k_v37.fasta<br clear="none">
>>> force_overwrite 1<br clear="none">
>>> format vcf<br clear="none">
>>> host <a rel="nofollow" shape="rect" target="_blank" href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a><br clear="none">
>>> input_file chr22-single.vcf<br clear="none">
>>> no_progress 1<br clear="none">
>>> output_file VEP_22.vcfout<br clear="none">
>>> polyphen b<br clear="none">
>>> port 3337<br clear="none">
>>> sift b<br clear="none">
>>> species homo_sapiens<br clear="none">
>>> stats HASH(0x2d671c0)<br clear="none">
>>> symbol 1<br clear="none">
>>> vcf 1<br clear="none">
>>> verbose 1<br clear="none">
>>><br clear="none">
>>> --------------------<br clear="none">
>>><br clear="none">
>>> Will only load v78 databases<br clear="none">
>>> No core-like databases found. Check your DB_VERSION (used '78')<br clear="none">
>>> No variation databases found<br clear="none">
>>> No funcgen databases found<br clear="none">
>>> No Compara databases found<br clear="none">
>>> No ancestral database found<br clear="none">
>>> No ontology database found<br clear="none">
>>> No production database or adaptor found<br clear="none">
>>><br clear="none">
>>> -------------------- WARNING ----------------------<br clear="none">
>>> MSG: homo_sapiens is not a valid species name (check DB and API version)<br clear="none">
>>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1200<br clear="none">
>>> CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 985<br clear="none">
>>> Date (localtime) = Thu Jul 16 22:52:00 2015<br clear="none">
>>> Ensembl API version = 78<br clear="none">
>>> ---------------------------------------------------<br clear="none">
>>><br clear="none">
>>> -------------------- EXCEPTION --------------------<br clear="none">
>>> MSG: Can not find internal name for species 'homo_sapiens'<br clear="none">
>>> STACK Bio::EnsEMBL::Registry::get_adaptor<br clear="none">
>>><br clear="none">
>>> /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:987<br clear="none">
>>> STACK main::connect_to_dbs<br clear="none">
>>><br clear="none">
>>> /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/<a rel="nofollow" shape="rect" target="_blank" href="http://variant_effect_predictor.pl:1161">variant_effect_predictor.pl:1161</a><br clear="none">
>>> STACK main::configure<br clear="none">
>>><br clear="none">
>>> /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/<a rel="nofollow" shape="rect" target="_blank" href="http://variant_effect_predictor.pl:766">variant_effect_predictor.pl:766</a><br clear="none">
>>> STACK toplevel<br clear="none">
>>> /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/<a rel="nofollow" shape="rect" target="_blank" href="http://variant_effect_predictor.pl:140">variant_effect_predictor.pl:140</a><br clear="none">
>>> Date (localtime) = Thu Jul 16 22:52:00 2015<br clear="none">
>>> Ensembl API version = 78<br clear="none">
>>> ---------------------------------------------------<br clear="none">
>>><br clear="none">
>>><br clear="none">
>>><br clear="none">
>>><br clear="none">
>>> On 9 June 2015 at 10:40, Nikolai Adamski (JIC)<br clear="none">
>>> <<a rel="nofollow" shape="rect" ymailto="mailto:Nikolai.Adamski@jic.ac.uk" target="_blank" href="javascript:return">Nikolai.Adamski@jic.ac.uk</a>> wrote:<br clear="none">
>>>><br clear="none">
>>>> Hi Will,<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> thank you for the quick answer!<br clear="none">
>>>><br clear="none">
>>>> Still puzzled though why it seems to have worked last week.<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> cheers<br clear="none">
>>>><br clear="none">
>>>> nikolai<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> From: <a rel="nofollow" shape="rect" ymailto="mailto:dev-bounces@ensembl.org" target="_blank" href="javascript:return">dev-bounces@ensembl.org</a> [mailto:<a rel="nofollow" shape="rect" ymailto="mailto:dev-bounces@ensembl.org" target="_blank" href="javascript:return">dev-bounces@ensembl.org</a>] On Behalf<br clear="none">
>>>> Of<br clear="none">
>>>> Will McLaren<br clear="none">
>>>> Sent: 09 June 2015 10:35<br clear="none">
>>>> To: Ensembl developers list<br clear="none">
>>>> Subject: Re: [ensembl-dev] VEP unable to connect to Ensembl Genomes<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> Hi Nikolai,<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> The release 80 databases are not yet available.<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> You may either use --offline to avoid checking the database connection,<br clear="none">
>>>> or<br clear="none">
>>>> "--db_version 79" to force VEP to connect to the release 79 databases.<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> Regards<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> Will McLaren<br clear="none">
>>>><br clear="none">
>>>> Ensembl Variation<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> On 9 June 2015 at 10:24, Nikolai Adamski (JIC)<br clear="none">
>>>> <<a rel="nofollow" shape="rect" ymailto="mailto:Nikolai.Adamski@jic.ac.uk" target="_blank" href="javascript:return">Nikolai.Adamski@jic.ac.uk</a>><br clear="none">
>>>> wrote:<br clear="none">
>>>><br clear="none">
>>>> Hi,<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> I used VEP on wheat data on Friday (5th of June) without problems<br clear="none">
>>>> (ensembl-tools-80)<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> perl <a rel="nofollow" shape="rect" target="_blank" href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -i input.vcf -o output.txt --cache<br clear="none">
>>>> --species triticum_aestivum --cache_version 26<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> I tried running more data today, but keep getting error message:<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> -------------------- WARNING ----------------------<br clear="none">
>>>><br clear="none">
>>>> MSG: triticum_aestivum is not a valid species name (check DB and API<br clear="none">
>>>> version)<br clear="none">
>>>><br clear="none">
>>>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1198<br clear="none">
>>>><br clear="none">
>>>> CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 983<br clear="none">
>>>><br clear="none">
>>>> Date (localtime) = Tue Jun 9 10:20:21 2015<br clear="none">
>>>><br clear="none">
>>>> Ensembl API version = 80<br clear="none">
>>>><br clear="none">
>>>> ---------------------------------------------------<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> -------------------- EXCEPTION --------------------<br clear="none">
>>>><br clear="none">
>>>> MSG: Can not find internal name for species 'triticum_aestivum'<br clear="none">
>>>><br clear="none">
>>>> STACK Bio::EnsEMBL::Registry::get_adaptor<br clear="none">
>>>><br clear="none">
>>>> /usr/users/celldev/adamskin/Downloads/ensembl-tools-release-80/scripts/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:985<br clear="none">
>>>><br clear="none">
>>>> STACK main::connect_to_dbs <a rel="nofollow" shape="rect" target="_blank" href="http://variant_effect_predictor.pl:1205">variant_effect_predictor.pl:1205</a><br clear="none">
>>>><br clear="none">
>>>> STACK main::configure <a rel="nofollow" shape="rect" target="_blank" href="http://variant_effect_predictor.pl:794">variant_effect_predictor.pl:794</a><br clear="none">
>>>><br clear="none">
>>>> STACK toplevel <a rel="nofollow" shape="rect" target="_blank" href="http://variant_effect_predictor.pl:142">variant_effect_predictor.pl:142</a><br clear="none">
>>>><br clear="none">
>>>> Date (localtime) = Tue Jun 9 10:20:21 2015<br clear="none">
>>>><br clear="none">
>>>> Ensembl API version = 80<br clear="none">
>>>><br clear="none">
>>>> ---------------------------------------------------<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> Using the --genomes flag results in the same error message.<br clear="none">
>>>><br clear="none">
>>>> Is the server down?<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> Many thanks for your help<br clear="none">
>>>><br clear="none">
>>>> cheers<br clear="none">
>>>><br clear="none">
>>>> nikolai<br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> _______________________________________________<br clear="none">
>>>> Dev mailing list <a rel="nofollow" shape="rect" ymailto="mailto:Dev@ensembl.org" target="_blank" href="javascript:return">Dev@ensembl.org</a><br clear="none">
>>>> Posting guidelines and subscribe/unsubscribe info:<br clear="none">
>>>> <a rel="nofollow" shape="rect" target="_blank" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br clear="none">
>>>> Ensembl Blog: <a rel="nofollow" shape="rect" target="_blank" href="http://www.ensembl.info/">http://www.ensembl.info/</a><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>><br clear="none">
>>>> _______________________________________________<br clear="none">
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>>>> Ensembl Blog: <a rel="nofollow" shape="rect" target="_blank" href="http://www.ensembl.info/">http://www.ensembl.info/</a><br clear="none">
>>>><br clear="none">
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>><br clear="none">
>><br clear="none">
>><br clear="none">
>> _______________________________________________<br clear="none">
>> Dev mailing list <a rel="nofollow" shape="rect" ymailto="mailto:Dev@ensembl.org" target="_blank" href="javascript:return">Dev@ensembl.org</a><br clear="none">
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><br clear="none">
><br clear="none">
><br clear="none">
> _______________________________________________<br clear="none">
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</div></div></blockquote></div><br clear="none"></div></div></td> </tr> </tbody> </table></div></td></tr></table>