<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><br></div><div><br></div><div>Hello Will, </div><div><br></div><div>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.<b> Is this what the write_cache option is intend to do ?</b> </div><div><br></div><div>I ran into a bit of trouble when using it, as </div><div> - 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 <a href="http://uswest.ensembl.org/info/docs/tools/vep/script/vep_example.html">http://uswest.ensembl.org/info/docs/tools/vep/script/vep_example.html</a> </div><div><br></div><div>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: </div><div><br></div><div>gzip: /.vep/homo_sapiens/77_GRCh38/1/2000001-3000000_var.gz: unexpected end of file</div><div>gzip: /.vep/homo_sapiens/77_GRCh38/1/3000001-4000000_var.gz: unexpected end of file</div><div>gzip: /.vep/homo_sapiens/77_GRCh38/1/11000001-12000000_var.gz: unexpected end of file</div><div><br></div><div>Have you seen this before ? </div><div><br></div><div>Also, I can’t get VEP to work with two different cache files - my ideal setup would be </div><div><br></div><div>a) <b>a system-wide cache</b> with pre-computed cache data from EnsEMBL </div><div>b)<b> a “by-user” cache</b> - 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. </div><div><br></div><div>Ideally, it would also be <b>possible to merge both caches</b> ( user + system-wide) - so other users can benefit from pre-calculated variations. </div><div><br></div><div><br></div><div>I’m in a multi-user environment, that’s why I am hesitant to have all users write to the same system-wide cache. </div><div><br></div><div>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 <font face="Menlo">—dir</font> and <font face="Menlo">—dir_cache</font> options can be used this way ... </div><div><br></div><div><div>Here’s my command line : </div><div><br></div><div><font face="Menlo">perl ensembl-tools-release-78/scripts/variant_effect_predictor/variant_effect_predictor.pl </font></div><div><font face="Menlo">—write_cache </font></div><div><font face="Menlo"> —verbose</font></div><div><font face="Menlo"> —cache </font></div><div><font face="Menlo"> —force_overwrite</font></div><div><font face="Menlo"> -i test.vcf -o test.out </font></div><div><font face="Menlo"> --dir_cache /gne/research/workspace/vogelj4/variant_effect_predictor/jensenmann/igis_cache/new_cache --cache_version 77 </font></div><div><font face="Menlo"> --species homo_sapiens </font></div><div><font face="Menlo"> --db_version 77</font></div><div><font face="Menlo"> --dir /gne/research/workspace/vogelj4/variant_effect_predictor/jensenmann/igis_cache/e77.1/VEP/ </font></div><div><font face="Menlo"> --fork 12</font></div></div><div><br></div><div><br></div><div>Thanks for this great tool ! </div><div><br></div><div> Jan </div><div><br></div><div><br></div><div><br></div><div><br></div><div><font face="Menlo"><br></font></div><div><br></div><div><br></div></body></html>