[ensembl-dev] Variant Effect Predictor error

[Radhika Bartaula]

Hi Will,
Thank you very much. It worked.

Regards,
Radhika
On Feb 4, 2015, at 4:17 AM, Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>> wrote:

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<http://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<mailto: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<http://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<mailto:mr6 at ebi.ac.uk>> <mr6 at ebi.ac.uk<mailto:mr6 at ebi.ac.uk>> wrote:

Public
database server


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