[ensembl-dev] VEP on Gorilla

Fri Jun 6 09:59:21 BST 2014

Hi Yuan,

SIFT is not available for gorilla. Currently supported species are:

Chicken, Cow, Dog, Human, Mouse, Pig, Rat and Zebrafish

If you remove sift from your options then it should work fine. However, the
code should warn and continue gracefully; there is a bug in the script that
I will fix.

Cheers

Will

On 6 June 2014 06:45, Yuan Chen <yuan at sanger.ac.uk> wrote:

> Yes, I am using Sanger cache, the config_file is
> : /lustre/scratch113/projects/g1k-fig/Gorilla/gorilla_ref/vcf_file/VEP/vep_config_file
>
> If I use your way, it works it doesn’t matter whether I put -species
> gorilla or gorilla_gorilla, but if I use my config file, although it point
> to same cache directory , but give error message :
>
> perl /nfs/users/nfs_y/yuan/sanger/src/svn/VEP/variant_effect_predictor.pl
> -i qasim_gtype.vcf -species gorilla -config vep_config_file
> 2014-06-06 05:57:53 - Read configuration from vep_config_file
> ERROR: Cache directory /data/blastdb/Ensembl/vep/gorilla/75 not found
> at /nfs/users/nfs_y/yuan/sanger/src/svn/VEP/variant_effect_predictor.pl
> line 993.
>
>
> OK, I think if I delete offline or change species from gorilla to
> gorilla_gorilla  in my config_file, this error has gone, but if I use -vcf
> I still got error : Can't call method "db" on unblessed reference at
> /nfs/team19/yuan/ensembl-checkout/ensembl-variation-75/modules/Bio/EnsEMBL/Variation/TranscriptVariation.pm
> line 322, <GEN0> line 9.
>
> if I remove -vcf,  it works ok.
>
>
> yuan
>
> On 5 Jun 2014, at 10:27, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
> Hi Yuan,
>
> I don't see this error message - are you using the Sanger cache?
>
> Which options are you using?
>
> My output is below.
>
> Regards
>
> Will
>
> > perl variant_effect_predictor.pl -i yuan.vcf -cache -species gorilla
> -force -dir /data/blastdb/Ensembl/vep -everything -no_progress
> 2014-06-05 10:25:26 - Read existing cache info
> 2014-06-05 10:25:26 - Auto-detected FASTA file in cache directory
> 2014-06-05 10:25:26 - Checking/creating FASTA index
> 2014-06-05 10:25:26 - INFO: Database will be accessed when using --sift;
> consider using the complete cache containing sift data (see documentation
> for details)
> 2014-06-05 10:25:26 - INFO: Database will be accessed when using
> --polyphen; consider using the complete cache containing polyphen data (see
> documentation for details)
> 2014-06-05 10:25:26 - Starting...
> 2014-06-05 10:25:26 - INFO: --sift is not available for this species
> 2014-06-05 10:25:26 - INFO: --polyphen is not available for this species
> 2014-06-05 10:25:26 - Detected format of input file as vcf
> 2014-06-05 10:25:26 - Read 1 variants into buffer
> 2014-06-05 10:25:26 - Checking for existing variations
> 2014-06-05 10:25:26 - WARNING: Could not find variation cache for
> 11:91000001-92000000
> 2014-06-05 10:25:26 - Reading transcript data from cache and/or database
> 2014-06-05 10:25:26 - Retrieved 32 transcripts (0 mem, 32 cached, 0 DB, 0
> duplicates)
> 2014-06-05 10:25:26 - Analyzing chromosome 11
> 2014-06-05 10:25:26 - Analyzing variants
> 2014-06-05 10:25:26 - Calculating consequences
> 2014-06-05 10:25:26 - Processed 1 total variants (1 vars/sec, 1 vars/sec
> total)
> 2014-06-05 10:25:26 - Wrote stats summary to
> variant_effect_output.txt_summary.html
> 2014-06-05 10:25:26 - Finished!
>
> > grep -v # variant_effect_output.txt
> 11_91630310_A/G 11:91630310     G       ENSGGOG00000014840
>  ENSGGOT00000014893      Transcript      missense_variant        55      55
>         19      T/A     Acc/Gcc -
> STRAND=1;SYMBOL=FOLR4;HGVSc=ENSGGOT00000014893.2:c.55A>G;DOMAINS=Pfam_domain:PF03024,Cleavage_site_(Signalp):Sigp;HGVSp=ENSGGOP00000014480.2:p.Thr19Ala;SYMBOL_SOURCE=Uniprot_gn;ENSP=ENSGGOP00000014480;EXON=1/4;BIOTYPE=protein_coding;CANONICAL=YES
>
>
> On 5 June 2014 03:38, Yuan Chen <yuan at sanger.ac.uk> wrote:
>
>> Hi Will,
>>
>> I have a gorilla variant :
>> 11      91630310        .       A       G
>>
>> if I use species gorilla_gorilla, then I got error message :
>> Can't call method "db" on unblessed reference at
>> /nfs/team19/yuan/ensembl-checkout/ensembl-variation-75/modules/Bio/EnsEMBL/Variation/TranscriptVariation.pm
>> line 322, <GEN0> line 9
>>
>> if I use other species, such as homo_sapiens, then it’s fine with same
>> config file, only species is different.
>> WEB tool on gorilla runs fine as well.
>>
>> Could you help on this please.
>>
>> yuan
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