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

[Will McLaren]

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

Regards
Will


On 15 September 2014 14:26, Guillermo Marco Puche <
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 (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> 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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