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"No cache found for homo_sapiens, version 105", but the latest version is 112 #1716

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jielab opened this issue Jul 6, 2024 · 6 comments
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@jielab
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jielab commented Jul 6, 2024

Hi, there:

When I run VEP, I got MSG: ERROR: No cache found for homo_sapiens, version 105.

However, the latest version is https://ftp.ensembl.org/pub/release-112/, and I downloaded it.

So, how could I change VEP to use this latest release cache?

Your help would be greatly appreciated!

Thank you & best regards,
Jie

@dglemos dglemos self-assigned this Jul 8, 2024
@dglemos
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dglemos commented Jul 8, 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.

@jielab
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jielab commented Jul 9, 2024 via email

@dglemos
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dglemos commented Jul 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.

@jielab
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jielab commented Jul 20, 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

@dglemos
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dglemos commented Aug 13, 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

@dglemos
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dglemos commented Sep 10, 2024

I'm going to close this issue, if you have more questions please open a new one.

Best wishes,
Diana

@dglemos dglemos closed this as completed Sep 10, 2024
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