-
Notifications
You must be signed in to change notification settings - Fork 154
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
"No cache found for homo_sapiens, version 105", but the latest version is 112 #1716
Comments
Hi @jielab, |
Hi, there:
It now works after I added --cache_version 112.
Below is my full VEP script. I used source activate ensembl-vep to call vep.
vep -i tmp3.vcf.gz --vcf -o tmp4.vcf --offline --cache --dir $dir/data/vep --cache_version 112 --species homo_sapiens --format vcf --vcf --force_overwrite --overlaps --sift b --symbol --canonical --pick --stats_text high_conf_vep.stats --assembly GRCh38
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.
Just curious, now with tools such as alpha-fold and primateAI-3D, is VEP also going to AI soon?
Best regards,
jie
发件人: Diana Lemos ***@***.***>
发送时间: 2024年7月8日 16:15
收件人: Ensembl/ensembl-vep ***@***.***>
抄送: Jie Huang ***@***.***>; Mention ***@***.***>
主题: Re: [Ensembl/ensembl-vep] "No cache found for homo_sapiens, version 105", but the latest version is 112 (Issue #1716)
Hi @jielab <https://github.com/jielab> ,
Can you please send the command you are running?
The error message indicates vep is trying to use the cache version 115. To use a different version you can use the option --cache_version <https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_cache_version> .
—
Reply to this email directly, view it on GitHub <#1716 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGNS6773CUQCRBMPFQKEN33ZLJC75AVCNFSM6AAAAABKONVDHWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJTGMZDKMJQGI> .
You are receiving this because you were mentioned. <https://github.com/notifications/beacon/AGNS67ZTTRK4QJ6ZWUDALJLZLJC75A5CNFSM6AAAAABKONVDHWWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTUD5SUS4.gif> Message ID: ***@***.*** ***@***.***> >
|
I'm glad it works now.
This is a BioPerl warning. The issue has been reported here: bioperl/bioperl-live#355 |
Thanks! How to check if my vep code is also for version 112? Again, our IT admin person installed vep through conda, very recently. Best regards, |
The VEP version should be in the output header. Best wishes, |
I'm going to close this issue, if you have more questions please open a new one. Best wishes, |
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
The text was updated successfully, but these errors were encountered: