<div dir="ltr">Hi Nikolas,<div><br></div><div>Seems like a network issue; you can just download the latest version of VEP manually and run the installer to get the API.</div><div><br></div><div><a href="http://www.ensembl.org/info/docs/tools/vep/script/index.html">http://www.ensembl.org/info/docs/tools/vep/script/index.html</a><br></div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 28 July 2015 at 16:21, Nikolas Pontikos <span dir="ltr"><<a href="mailto:n.pontikos@ucl.ac.uk" target="_blank">n.pontikos@ucl.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks Will, however I get an error when I run the update:<div><br></div><div><div>cd ensembl/src/ensembl-tools/scripts/variant_effect_predictor</div><div><br></div><div>perl INSTALL.pl --UPDATE</div><div><br></div><div>Hello! This installer is configured to install v78 of the Ensembl API for use by the VEP.</div><div>It will not affect any existing installations of the Ensembl API that you may have.</div><div><br></div><div>It will also download and install cache files from Ensembl's FTP server.</div><div><br></div><div>Checking for newer version of the VEP</div><div>malformed JSON string, neither array, object, number, string or atom, at character offset 0 (before "<!DOCTYPE html>\n<!-...") at INSTALL.pl line 121.</div><div>[rmhanpo@pchuckle:/cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor$] vim INSTALL.pl +121</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On 27 July 2015 at 13:27, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Nikolas,<div><br></div><div>The VEP INSTALL.pl script offers an update option, simply run:</div><div><br></div><div>perl INSTALL.pl --UPDATE</div><span><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></span></div><div class="gmail_extra"><br><div class="gmail_quote"><span>On 25 July 2015 at 11:45, Nikolas Pontikos <span dir="ltr"><<a href="mailto:n.pontikos@ucl.ac.uk" target="_blank">n.pontikos@ucl.ac.uk</a>></span> wrote:<br></span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>Hello Magali,<br>
<br>
There is no particular reason except that I haven't gotten round to<br>
updating our installation.<br>
Incidentally, what is the most straightforward way of doing an update?<br>
<br>
Thanks,<br>
<br>
Nikolas.<br>
</span><div><div><span><br>
<br>
On 17 July 2015 at 11:33, mag <<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>> wrote:<br>
> Hi Nikolas,<br>
><br>
> Apologies for the misleading information, we officially support 2 releases<br>
> at one given time, the current one and the previous one<br></span>
> <a href="http://grch37.ensembl.org/info/data/mysql.html" rel="noreferrer" target="_blank">http://grch37.ensembl.org/info/data/mysql.html</a><div><div><br>
><br>
> The release 79 databases have not yet been cleared up following release 81,<br>
> but we cannot guarantee they will remain available much longer, as this<br>
> depends on the space available on the server.<br>
><br>
> May I ask if there is a particular reason you are using version 78 and not a<br>
> more recent one?<br>
><br>
><br>
> Regards,<br>
> Magali<br>
><br>
><br>
> On 17/07/2015 10:56, mag wrote:<br>
>><br>
>> Hi Nikolas,<br>
>><br>
>> We are currently maintaining 3 releases worth of databases on the<br>
>> dedicated GRCh37 MySQL server.<br>
>> As 81 was released yesterday, 78 has now been removed.<br>
>> You can still access releases 79, 80 and 81 for the GRCh37 assembly.<br>
>><br>
>><br>
>> Hope this helps,<br>
>> Magali<br>
>><br>
>> On 17/07/2015 10:46, Nikolas Pontikos wrote:<br>
>>><br>
>>> Yes I've just witnessed the same problem.<br>
>>> Code used to work, nothing changed and stopped working.<br>
>>> Something might have changed on the server side.<br>
>>> Adding the --offline flag seems to have fixed it.<br>
>>> This is the error message below:<br>
>>><br>
>>><br>
>>> #----------------------------------#<br>
>>> # ENSEMBL VARIANT EFFECT PREDICTOR #<br>
>>> #----------------------------------#<br>
>>><br>
>>> version 78<br>
>>><br></div></div>
>>> By Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)<span><br>
>>><br>
>>> Configuration options:<br>
>>><br>
>>> assembly GRCh37<br>
>>> canonical 1<br>
>>> check_alleles 1<br>
>>> check_existing 1<br>
>>> core_type core<br>
>>> database 1<br>
>>> dir /home/rmhanpo/.vep<br>
>>> dir_plugins /home/rmhanpo/.vep/Plugins<br>
>>> fasta<br>
>>><br>
>>> /scratch2/vyp-scratch2/reference_datasets/human_reference_sequence/human_g1k_v37.fasta<br>
>>> force_overwrite 1<br>
>>> format vcf<br></span>
>>> host <a href="http://ensembldb.ensembl.org" rel="noreferrer" target="_blank">ensembldb.ensembl.org</a><div><div><br>
>>> input_file chr22-single.vcf<br>
>>> no_progress 1<br>
>>> output_file VEP_22.vcfout<br>
>>> polyphen b<br>
>>> port 3337<br>
>>> sift b<br>
>>> species homo_sapiens<br>
>>> stats HASH(0x2d671c0)<br>
>>> symbol 1<br>
>>> vcf 1<br>
>>> verbose 1<br>
>>><br>
>>> --------------------<br>
>>><br>
>>> Will only load v78 databases<br>
>>> No core-like databases found. Check your DB_VERSION (used '78')<br>
>>> No variation databases found<br>
>>> No funcgen databases found<br>
>>> No Compara databases found<br>
>>> No ancestral database found<br>
>>> No ontology database found<br>
>>> No production database or adaptor found<br>
>>><br>
>>> -------------------- WARNING ----------------------<br>
>>> MSG: homo_sapiens is not a valid species name (check DB and API version)<br>
>>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1200<br>
>>> CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 985<br>
>>> Date (localtime) = Thu Jul 16 22:52:00 2015<br>
>>> Ensembl API version = 78<br>
>>> ---------------------------------------------------<br>
>>><br>
>>> -------------------- EXCEPTION --------------------<br>
>>> MSG: Can not find internal name for species 'homo_sapiens'<br>
>>> STACK Bio::EnsEMBL::Registry::get_adaptor<br>
>>><br>
>>> /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:987<br>
>>> STACK main::connect_to_dbs<br>
>>><br></div></div>
>>> /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl:1161" rel="noreferrer" target="_blank">variant_effect_predictor.pl:1161</a><br>
>>> STACK main::configure<br>
>>><br>
>>> /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl:766" rel="noreferrer" target="_blank">variant_effect_predictor.pl:766</a><br>
>>> STACK toplevel<br>
>>> /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl:140" rel="noreferrer" target="_blank">variant_effect_predictor.pl:140</a><span><br>
>>> Date (localtime) = Thu Jul 16 22:52:00 2015<br>
>>> Ensembl API version = 78<br>
>>> ---------------------------------------------------<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> On 9 June 2015 at 10:40, Nikolai Adamski (JIC)<br></span><span>
>>> <<a href="mailto:Nikolai.Adamski@jic.ac.uk" target="_blank">Nikolai.Adamski@jic.ac.uk</a>> wrote:<br>
>>>><br>
>>>> Hi Will,<br>
>>>><br>
>>>><br>
>>>><br>
>>>> thank you for the quick answer!<br>
>>>><br>
>>>> Still puzzled though why it seems to have worked last week.<br>
>>>><br>
>>>><br>
>>>><br>
>>>> cheers<br>
>>>><br>
>>>> nikolai<br>
>>>><br>
>>>><br>
>>>><br></span>
>>>> From: <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>] On Behalf<span><br>
>>>> Of<br>
>>>> Will McLaren<br>
>>>> Sent: 09 June 2015 10:35<br>
>>>> To: Ensembl developers list<br>
>>>> Subject: Re: [ensembl-dev] VEP unable to connect to Ensembl Genomes<br>
>>>><br>
>>>><br>
>>>><br>
>>>> Hi Nikolai,<br>
>>>><br>
>>>><br>
>>>><br>
>>>> The release 80 databases are not yet available.<br>
>>>><br>
>>>><br>
>>>><br>
>>>> You may either use --offline to avoid checking the database connection,<br>
>>>> or<br>
>>>> "--db_version 79" to force VEP to connect to the release 79 databases.<br>
>>>><br>
>>>><br>
>>>><br>
>>>> Regards<br>
>>>><br>
>>>><br>
>>>><br>
>>>> Will McLaren<br>
>>>><br>
>>>> Ensembl Variation<br>
>>>><br>
>>>><br>
>>>><br>
>>>> On 9 June 2015 at 10:24, Nikolai Adamski (JIC)<br></span>
>>>> <<a href="mailto:Nikolai.Adamski@jic.ac.uk" target="_blank">Nikolai.Adamski@jic.ac.uk</a>><span><br>
>>>> wrote:<br>
>>>><br>
>>>> Hi,<br>
>>>><br>
>>>><br>
>>>><br>
>>>> I used VEP on wheat data on Friday (5th of June) without problems<br>
>>>> (ensembl-tools-80)<br>
>>>><br>
>>>><br>
>>>><br></span>
>>>> perl <a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a> -i input.vcf -o output.txt --cache<span><br>
>>>> --species triticum_aestivum --cache_version 26<br>
>>>><br>
>>>><br>
>>>><br>
>>>> I tried running more data today, but keep getting error message:<br>
>>>><br>
>>>><br>
>>>><br>
>>>> -------------------- WARNING ----------------------<br>
>>>><br>
>>>> MSG: triticum_aestivum is not a valid species name (check DB and API<br>
>>>> version)<br>
>>>><br>
>>>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1198<br>
>>>><br>
>>>> CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 983<br>
>>>><br>
>>>> Date (localtime) = Tue Jun 9 10:20:21 2015<br>
>>>><br>
>>>> Ensembl API version = 80<br>
>>>><br>
>>>> ---------------------------------------------------<br>
>>>><br>
>>>><br>
>>>><br>
>>>> -------------------- EXCEPTION --------------------<br>
>>>><br>
>>>> MSG: Can not find internal name for species 'triticum_aestivum'<br>
>>>><br>
>>>> STACK Bio::EnsEMBL::Registry::get_adaptor<br>
>>>><br>
>>>> /usr/users/celldev/adamskin/Downloads/ensembl-tools-release-80/scripts/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:985<br>
>>>><br></span><span>
>>>> STACK main::connect_to_dbs <a href="http://variant_effect_predictor.pl:1205" rel="noreferrer" target="_blank">variant_effect_predictor.pl:1205</a><br>
>>>><br>
>>>> STACK main::configure <a href="http://variant_effect_predictor.pl:794" rel="noreferrer" target="_blank">variant_effect_predictor.pl:794</a><br>
>>>><br></span>
>>>> STACK toplevel <a href="http://variant_effect_predictor.pl:142" rel="noreferrer" target="_blank">variant_effect_predictor.pl:142</a><span><br>
>>>><br>
>>>> Date (localtime) = Tue Jun 9 10:20:21 2015<br>
>>>><br>
>>>> Ensembl API version = 80<br>
>>>><br>
>>>> ---------------------------------------------------<br>
>>>><br>
>>>><br>
>>>><br>
>>>> Using the --genomes flag results in the same error message.<br>
>>>><br>
>>>> Is the server down?<br>
>>>><br>
>>>><br>
>>>><br>
>>>> Many thanks for your help<br>
>>>><br>
>>>> cheers<br>
>>>><br>
>>>> nikolai<br>
>>>><br>
>>>><br>
>>>> _______________________________________________<br></span>
>>>> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><span><br>
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>>>> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>>>><br>
>>>><br>
>>>><br>
>>>><br>
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>>>><br>
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>><br>
>><br>
>><br>
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><br>
><br>
><br>
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