[ensembl-dev] VEP on Gorilla

Will McLaren wm2 at ebi.ac.uk
Thu Jun 5 10:27:11 BST 2014


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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