[ensembl-dev] VEP on Gorilla

Fri Jun 6 10:26:18 BST 2014

Yes, that’s the problem.

Thanks for your help.

yuan
On 6 Jun 2014, at 09:59, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140606/bf1c3b86/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 2056 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140606/bf1c3b86/attachment.p7s>