[ensembl-dev] VEP error - mouse cache

[Will McLaren]

Hi Chris,

It looks like your API install is out of date - I don't know who maintains
these in /software/vertres/, but presumably they have not been updated
post-release (we sometimes put fixes in after the initial release).

Either get whoever maintains them to update, check out your own version
using CVS (see http://www.ensembl.org/info/docs/api/api_cvs.html) and
modify your PERL5LIB or use perl -I /path/to/me/ensembl-variation/modules,
or use the INSTALL.pl script included in the tarball available from the VEP
documentation page (
http://www.ensembl.org/info/docs/variation/vep/vep_script.html#download).

Any reason you're not using the latest version (2.7)?

Cheers

Will


On 7 November 2012 14:12, <cj5 at sanger.ac.uk> wrote:

> Hi,
>
> We are having problems running the VEP script version 2.4 in offline mode
> using the mouse cache, eg:
>
> cat mouse.vcf | variant_effect_predictor.pl --species mus_musculus --gene
> --hgnc --format vcf -o mouse.vep.txt --force_overwrite --cache
> --dir /lustre/scratch105/projects/g1k/ref/vep_cache --offline
>
> Can't call method "length" on unblessed reference at
> /software/vertres/lib/all/ensembl/66/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1758, <STDIN> line 11.
>
> The example vcf looks looks this:
>
> ##fileformat=VCFv4.1
> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled
> genotype likelihoods">
> ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand
> bias P-value">
> ##INFO=DP,1,Integer,"Total Depth"
> ##INFO=AC,-1,Integer,"Allele count in genotypes"
> ##INFO=AN,1,Integer,"Total number of alleles in called genotypes"
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  AJ
> 1       3000054 .       AGGGGGGGGGG     AGGGGGGGGGGG    36.5    PASS
>  AC=2;AN=34      GT:PL:DP:SP:GQ  1/1:74,39,0:13:0:99
>
> It looks like a problem with the cache itself, because if we simply change
> the position 3000054  to 13000054 (for example), it works. We
> tried downloading and re-installing the cache files but the problem
> persists. Could you please advise?
>
> Thanks
> Chris
>
>
>
>
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