[ensembl-dev] Problems using VEP cache with github version

Sarah Hunt seh at ebi.ac.uk
Fri Mar 31 15:17:18 BST 2017


Hi Hans,

Have you forgotten to include --offline when using new VEP? This will 
trigger the use of cache files.

Best wishes,

Sarah

On 28/03/2017 22:34, Hans Vasquez-Gross wrote:
> Hi ENSEMBL,
>
> I have successfully been using ensembl tool release 75 for a while. 
> Now, I'm planning to start using the github version because of the 
> speed increase as well as new features.
>
> However, I am having trouble running VEP.  I get the following error.
>
>
> ernie-sears:ensembl-vep_git_beta havasquezgross$ ./vep.pl 
> <http://vep.pl/> --species triticum_aestivum -i 
> Josh_mut_v4.mapspart2.HetMinCov3HetMinPer15HomMinCov2.vcf -o 
> Josh_mut_v4.mapspart2.HetMinCov3HetMinPer15HomMinCov2.vep.vcf --fork 4 
> --db_version 34 --assembly TGACv1 --force_overwrite
> WARNING: Chromosome TGACv1_scaffold_001462_1AL not found in annotation 
> sources or synonyms on line 1
>
> WARNING: Chromosome TGACv1_scaffold_001462_1AL not found in annotation 
> sources or synonyms on line 2
>
> WARNING: Chromosome TGACv1_scaffold_001462_1AL not found in annotation 
> sources or synonyms on line 3
>
> WARNING: Chromosome TGACv1_scaffold_001462_1AL not found in annotation 
> sources or synonyms on line 4
>
> WARNING: Chromosome TGACv1_scaffold_001462_1AL not found in annotation 
> sources or synonyms on line 5
>
> WARNING: Chromosome TGACv1_scaffold_001462_1AL not found in annotation 
> sources or synonyms on line 6
>
>
> However, looking at the VEP cache, this folder is actually present. Do 
> you have any suggestions why this error could be showing up?
>
> ernie-sears:TGACv1_scaffold_001462_1AL havasquezgross$ pwd
> /Users/havasquezgross/.vep/triticum_aestivum/34_TGACv1/TGACv1_scaffold_001462_1AL
> ernie-sears:TGACv1_scaffold_001462_1AL havasquezgross$ ls -1
> 1-1000000.gz
> 1-1000000_var.gz
>
>
> I also have a symlink in the .vep/triticum_aestivum folder which 
> points the directory 34_TGACv1 to 34 as well, so I can run with the 
> old release 75 version which I have been using for years.  Running 
> with release 75 doesn't print this same warning and produces results.
>
> time ./variant_effect_predictor.pl 
> <http://variant_effect_predictor.pl/> -species triticum_aestivum -i 
> v41.mapspart2.HetMinCov3HetMinPer15HomMinCov2.vcf -o 
> v41.mapspart2.HetMinCov3HetMinPer15HomMinCov2.vep.vcf --fork 4 
> --offline --db_version 34 --force_overwrite --compress gzcat --vcf
> [...clip...]
> 2017-03-27 15:22:32 - Writing output
> 2017-03-27 15:22:32 - Processed 239683 total variants (585 vars/sec, 
> 781 vars/sec total)
> 2017-03-27 15:22:34 - Wrote stats summary to 
> v41.mapspart2.HetMinCov3HetMinPer15HomMinCov2.vep.vcf_summary.html
> 2017-03-27 15:22:34 - Finished!
>
> real5m9.791s
> user17m47.120s
> sys5m17.075s
>
> Thank you,
> -Hans
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20170331/b31a63d1/attachment.html>


More information about the Dev mailing list