[ensembl-dev] Variant Effect Predictor error

[Will McLaren]

Hello,

Ensembl Genomes use different software version numbers to Ensembl; you
should be able to use your wheat cache using --cache_version 25, e.g.

perl variant_effect_predictor.pl -i
/berber/radhika/seq_for_assaf/pileup_on_rmdup/Zavitan_var.flt_d6_a4.vcf
--species
triticum_aestivum --cache --cache_version 25 --genomes

Regards

Will McLaren
Ensembl Variation


On 3 February 2015 at 22:09, Radhika Bartaula <rb11 at wildcats.unh.edu> wrote:

>  Hi Magali,
> Thank you very much for quick response. I did try with the -genomes option
> but still getting the error below.
>
>  UNIVERSAL->import is deprecated and will be removed in a future perl at
> /home/radhika/ensembl-tools-release-78/scripts/variant_effect_predictor/Bio/Tree/TreeFunctionsI.pm
> line 94.
>
>  ERROR: No cache found for triticum_aestivum, version 78
>
>  Based on the comments found at the link, I thought it might be because
> of the version issue.
> http://comments.gmane.org/gmane.science.biology.ensembl.devel/9198
>
>  So, I changed the version to 77, this is the error I get when I change
> the version.
>
>  perl variant_effect_predictor.pl -i
> /berber/radhika/seq_for_assaf/mpileup_on_rmdup/Zavitan_var.flt_d6_a4.vcf
> -genomes --species triticum_aestivum --cache -db_version 77
>
>  UNIVERSAL->import is deprecated and will be removed in a future perl at
> /home/radhika/ensembl-tools-release-78/scripts/variant_effect_predictor/Bio/Tree/TreeFunctionsI.pm
> line 94.
>
>  For triticum_aestivum_core_24_77_1 there is a difference in the software
> release (78) and the database release (77). You should update one of these
> to ensure that your script does not crash.
> For triticum_aestivum_variation_24_77_1 there is a difference in the
> software release (78) and the database release (77). You should update one
> of these to ensure that your script does not crash.
> ERROR: No cache found for triticum_aestivum, version 77
>
>  Thank you,
> Radhika
>
>
>
>   On Feb 3, 2015, at 4:46 PM, <mr6 at ebi.ac.uk> <mr6 at ebi.ac.uk> wrote:
>
> Public
> database server
>
>
>
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