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

[Hans Vasquez-Gross]

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 --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 -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!

real 5m9.791s
user 17m47.120s
sys 5m17.075s

Thank you,
-Hans
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