Comments (5)
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.
from ensembl-vep.
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.
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.
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.
Related Issues (20)
- --individual_zyg ind or all option triggers error. HOT 16
- CDS coordinate misalignment for some genes in VEP version 112 HOT 4
- Synonyms file does not work in the offline mode HOT 6
- Cant Install plugins HOT 4
- VEP112 predicts "inframe_insertion, stop_retained_variant" in cases where previously was predicted as "frameshift_variant, stop_gained" HOT 4
- Q: How to filter variants by a specific feature before --pick_order is applied? HOT 5
- `0` does not work as a variant identifier HOT 3
- StructuralVariantOverlap Hanging Indefinitely HOT 1
- issue specifiying cache dir (-d) and downloading files HOT 2
- Seeking clarity on --fields vs --custom usage HOT 4
- Request for Documentation and Containerization of Bio::EnsEMBL::XS Module for VEP to run faster. HOT 3
- filter_vep on HGNC_ID HOT 5
- SpliceAI plugin update please HOT 1
- VEP installation can not install Bio::DB:HTS module HOT 2
- ERROR: Can't detect input format HOT 2
- Document --max_sv_size command line default HOT 1
- Transcript blocklist / allowlists or option for max transcripts HOT 3
- Custom bigwig annotation not working for insertion variants HOT 2
- HGVS C dot not using right most aligned option
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from ensembl-vep.