[ensembl-dev] VEP: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match

[Guillermo Marco Puche]

Hello Will,

Ok that makes perfect sense.
Thank you for help as always Will.

Best regards,
Guillermo.

El 15/09/14 a las #4, Will McLaren escribió:
> Hi,
>
> It seems we haven't made available on our FTP site the dumps for *_76_37.
>
> The data is in fact identical to *_75_37 so you've a couple of solutions:
>
> 1) Point VEP to the 75 database (--db_version) and the 76 cache 
> (--cache_version)
>
> 2) Create *_76_37 databases with the *_75_37 data and patch the 
> schemas to 76 using ensembl/misc-scripts/schema_patcher.pl 
> <http://schema_patcher.pl>
>
> Regards
> Will
>
>
> On 15 September 2014 14:26, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Hello Will,
>
>     Indeed I run a local Ensembl installation. I've installed
>     homo_sapiens_*_76_38 that's why I'm getting the error. It was a
>     missunderstading from my part. I guess it's time to move to GRCh38.
>     Anyways I was trying to find homo_sapiens_*_76_37 MySQL links for
>     download but I just find homo_sapiens_*_76_38 on FTP server.
>
>     Could you give me a link to a mirror for homo_sapiens_*_76_37?
>
>     Thank you.
>
>     Best regards,
>     Guillermo.
>
>     El 15/09/14 a las #4, Will McLaren escribió:
>>     Hi Guillermo,
>>
>>     Are you also running your own database server?
>>
>>     The GRCh37 v76 databases are hosted on a different port on
>>     ensembldb.ensembl.org <http://ensembldb.ensembl.org> (3337); to
>>     get the VEP to use this you can add the flag --port 3337 to your
>>     command line. If you don't use the DB (most VEP functionality
>>     does not use the DB at all, see
>>     http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations),
>>     you can bypass this completely and use --offline. See
>>     http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly
>>     for more details.
>>
>>     If you are using your own DB server then you will need to make
>>     sure you have mirrored the correct human databases; you should
>>     have homo_sapiens_*_76_37 (* being core, variation and funcgen).
>>
>>     HTH
>>
>>     Will McLaren
>>     Ensembl Variation
>>
>>
>>     On 15 September 2014 09:04, Guillermo Marco Puche
>>     <guillermo.marco at sistemasgenomicos.com
>>     <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>>         I forgot to mention than I've already tried to specify
>>         assembly with VEP "--assembly" flag:
>>
>>         ERROR: Assembly version specified by --assembly (GRCh37) and
>>         assembly.default meta key (GRCh38) do not match
>>
>>         El 15/09/14 a las #4, Guillermo Marco Puche escribió:
>>>         Hello,
>>>
>>>         I installed Ensembl 76 on my local server. I'm not ready yet
>>>         to annotate variants vs GRCh38.
>>>         I thought that ensembl 76 version supports both GRCh37 and
>>>         GRCh38. I downloaded 76 vep cache for GRCh37:
>>>
>>>         ftp://ftp.ensembl.org/pub/release-76/variation/VEP/homo_sapiens_merged_vep_76_GRCh37.tar.gz
>>>
>>>         I get the following error:
>>>
>>>         *ERROR: Cache assembly version (GRCh37) and database or
>>>         selected assembly version (GRCh38) do not match.**
>>>         *
>>>         I got a bit confused since I saw both cache for GRCh37/38, I
>>>         would like to know if in Ensembl 76 I can stilll annotate
>>>         with GRCh37 or I just have to move asap to GRCh38 to use 76
>>>         version.
>>>
>>>         Thank you.
>>>
>>>         Best regards,
>>>         Guillermo.
>>>
>>>
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>>
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