[ensembl-dev] VEP not showing available cell types

[Will McLaren]

Hi Sid,

I suspect there is a problem with your cache, perhaps it did not extract
correctly.

You should have a file named "info.txt" in your
[cache_dir]/homo_sapiens/71/ , where [cache_dir] is wherever your cache was
installed, typically $HOME/.vep/ .

The file looks like this for release 71:

# CACHE UPDATED 2013-04-02 22:03:30
host    ens-staging
port    3306
user    ensro
build   all
regulatory      1
sift    b
polyphen        b
cell_types
 HeLa-S3,GM06990,U2OS,CD4,IMR90,HL-60,HepG2,Lymphoblastoid,CD133,CD36,K562,GM12878,HUVEC,NHEK,H1ESC,MultiCell,K562b,NH-A,HSMM,HMEC,A549,AG04449,AG04450,AG09309,AG09319,AG10803,Caco-2,Chorion,CMK,GM10847,GM12801,GM12864,GM12865,GM12872,GM12873,GM12874,GM12875,GM12891,GM12892,GM15510,GM18505,GM18507,GM18526,GM18951,GM19099,GM19193,GM19238,GM19239,GM19240,H7ESC,H9ESC,HAEpiC,HCF,HCM,HCPEpiC,HCT116,HEEpiC,HEK293b,HEK293,HepG2b,HGF,HIPEpiC,HNPCEpiC,HRCEpiC,HRE,HRPEpiC,Jurkat,LHSR,MCF7,Medullo,Melano,NB4,NHBE,NHDF-neo,NHLF,NT2-D1,Panc1,PanIslets,PFSK1,SAEC,SKMC,SKNMC,SKNSHRA,Th1,Th2,WERIRB1,RPTEC,ProgFib,HSMMtube,Osteobl,MCF10A-Er-Src,HPAEpiC,Fibrobl,GM12878-XiMat,BJ
sift_version    sift5.0.2
polyphen_version        2.2.2
variation_cols
 variation_name,failed,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,AFR,AMR,ASN,EUR

You could also check that it is working using --database in place of
--cache (but only to get the cell_type list!!!).

Regards

Will


On 14 May 2013 14:58, Siddharth Sethi <s.sethi at har.mrc.ac.uk> wrote:

>  Hi,
>
>
>
> I am trying to get the available cell types for Humans, but VEP is not
> printing the cell types when used –cell_type list
>
>
>
> ERROR: cell type list not recognised; available cell types are:
>
>
>
> This is command :
>
> perl EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/
> variant_effect_predictor.pl --cache -species homo_sapiens --regulatory
> -cell_type list
>
>
>
>
>
> Also,  it prints : Database will be accessed when using --regulatory;
> consider using the complete cache containing regulatory data.
>
> Can you please tell me what is the complete cache. I downloaded the cache
> files using the installer , so it should not access the database for
> regulatory.
>
>
>
> Thank you.
>
>
>
> Regards,
>
> Sid
>
>
>
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