[ensembl-dev] Variant effect predictor - write_cache option

[Jan Vogel]

Hello Will, 

I’m annotating some large scale data and I was thinking to create my own cache with the —write_cache option - my idea is that everytime I annotate a VCF, I add the variations, which have not been cached preciously, to the cache. Is this what the write_cache option is intend to do ? 

I ran into a bit of trouble when using it, as 
 - I had the same CODE ref exception from Storable.pm  ( fixed it with your —no_adaptor_cache option) - might be a good idea to add this to http://uswest.ensembl.org/info/docs/tools/vep/script/vep_example.html 

I also run into trouble when forking the script - it seems to me that there is a race condition, and that the forking processes are modifying the same cache files - so I end up with corrupted cache, and error message like: 

gzip: /.vep/homo_sapiens/77_GRCh38/1/2000001-3000000_var.gz: unexpected end of file
gzip: /.vep/homo_sapiens/77_GRCh38/1/3000001-4000000_var.gz: unexpected end of file
gzip: /.vep/homo_sapiens/77_GRCh38/1/11000001-12000000_var.gz: unexpected end of file

Have you seen this before ? 

Also, I can’t get VEP to work with two different cache files - my ideal setup would be 

a) a system-wide cache with pre-computed cache data from EnsEMBL 
b) a “by-user”  cache - once a user computed a single variation which is not in the system-wide cache, it would be great to add it to the user-cache - so it does not get re-computed. 

Ideally, it would also be possible to merge both caches ( user + system-wide) - so other users can benefit from pre-calculated variations. 


I’m in a multi-user environment, that’s why I am hesitant to have all users write to the same system-wide cache. 

Do such options currently exist and did I just not find them ? Or am I running VEP the wrong way ? I was hoping that the —dir and —dir_cache options can be used this way ... 

Here’s my command line : 

perl ensembl-tools-release-78/scripts/variant_effect_predictor/variant_effect_predictor.pl 
—write_cache 
   —verbose
       —cache 
        —force_overwrite
             -i test.vcf -o test.out 
                --dir_cache /gne/research/workspace/vogelj4/variant_effect_predictor/jensenmann/igis_cache/new_cache --cache_version 77 
                  --species homo_sapiens 
                     --db_version 77
                         --dir /gne/research/workspace/vogelj4/variant_effect_predictor/jensenmann/igis_cache/e77.1/VEP/ 
                              --fork 12


Thanks for this great tool ! 

   Jan 







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