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

[Will McLaren]

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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> --
>  ------------------------------
>
> *Guillermo Marco Puche*
>
> Bioinformatician, Computer Science Engineer
> Sistemas Genómicos S.L.
> Phone: +34 902 364 669 (Ext.777)
> Fax: +34 902 364 670
> www.sistemasgenomicos.com
>
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