[ensembl-dev] VEP error when using --regulatory flag

[Will McLaren]

Hello Sid,

It seems your attachment hasn't made it through - perhaps you could
paste the data into an email if it is small enough?

Thanks

Will McLaren
Ensembl Variation


On 19 April 2013 10:16, Siddharth Sethi <s.sethi at har.mrc.ac.uk> wrote:
> Hi ,
>
>
>
> I am using the latest version (v71) and using the VCF format (VCFv4.1)
> generated from GATK.
>
> The script breaks down when I use the –regulatory flag while it runs fine
> when I remove the flag.
>
> Also, it runs fine even with –regulatory for some VCF while it gives error
> with others, which is strange because all the VCF have been generated from
> the same pipeline.
>
> The script exits with the following error :
>
>
>
> 2013-04-18 16:28:54 - Read existing cache info
>
> 2013-04-18 16:28:54 - Starting...
>
> 2013-04-18 16:28:54 - Read 2125 variants into buffer
>
> 2013-04-18 16:28:54 - Reading transcript data from cache and/or database
>
> [==================================================================================================================================]
> [ 100% ]
>
> 2013-04-18 16:30:39 - Retrieved 50462 transcripts (0 mem, 52330 cached, 0
> DB, 1868 duplicates)
>
> 2013-04-18 16:30:39 - Reading regulatory data from cache and/or database
>
> [========>
> ]    [ 7% ]Can't call method "isa" on unblessed reference at
> EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm
> line 133, <GEN0> line 2125.
>
>
>
>
>
> This is the command :
>
> perl
> EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl
> -cache -i input.vcf -o VEP_output -species mus_musculus -format vcf --force
> -sift b –regulatory
>
>
>
> I have attached a test VCF file which is producing this error.
>
>
>
> Can you please help me in fixing this error
>
> I will appreciate any kind of help.
>
>
>
> Thank you
>
>
>
> Sid
>
> Bioinformatics
>
> MRC Harwell
>
> Mammalian Genetics Unit
>
> Harwell Science and Innovation Campus Oxfordshire
>
> OX11 0RD, UK
>
>
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please see:
> http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
>
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please see:
> http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
>
> _______________________________________________
> 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/
>