[ensembl-dev] VEP on Gorilla

[Yuan Chen]

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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