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dglemos avatar dglemos commented on August 15, 2024

Hi @jielab,
Can you please send the command you are running?
The error message indicates vep is trying to use the cache version 105. To use a different version you can use the option --cache_version.

from ensembl-vep.

jielab avatar jielab commented on August 15, 2024

from ensembl-vep.

dglemos avatar dglemos commented on August 15, 2024

I'm glad it works now.
We recommend using the same vep and cache version. Are you also using the vep code from version 112?

I do see a message: Possible precedence issue with control flow operator at /work/sph-huangj/.conda/envs/ensembl-vep/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805. Hope it does not cause any issue.

This is a BioPerl warning. The issue has been reported here: bioperl/bioperl-live#355
It shouldn't affect the output.

from ensembl-vep.

jielab avatar jielab commented on August 15, 2024

Thanks!

How to check if my vep code is also for version 112?

Again, our IT admin person installed vep through conda, very recently.
He followed all the instructions on VEP webpage.

Best regards,
Jie

from ensembl-vep.

dglemos avatar dglemos commented on August 15, 2024

The VEP version should be in the output header.
Here is an example:
##VEP="v112.0" API="v112" time="2024-04-04 16:15:29" cache="homo_sapiens/111_GRCh38" 1000genomes="phase3" COSMIC="98" ClinVar="202306" HGMD-PUBLIC="20204" assembly="GRCh38.p14" dbSNP="156" gencode="GENCODE 45" genebuild="2014-07" gnomADe="r2.1.1" gnomADg="v3.1.2" polyphen="2.2.3" regbuild="1.0" sift="6.2.1"

Best wishes,
Diana

from ensembl-vep.

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