[ensembl-dev] Is it a bug in ensembl_v79?

namchul ghim chulghim at gmail.com
Wed Mar 18 07:32:48 GMT 2015


After installing Ensembl_v79, I annotated vep cache with GRch37.
When doing so I got a following message:
Can't call method "impact" on an undefined value at
/mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor
/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2379.

When I checked the following source file, there is no definition of
imapct() function. There is only function name in the same line.
Isn't that a bug?

Also, in same condition, annotating only vep cache with GRCh38 version was
successful.

What is going on?

Additionally, when I was annotating vep cache with GRCh38 version, there is
a warning message in cache file.
The warning message is as follow:
WARNING: Could not find variation cache for 22:51000001-52000000
WARNING: Could not find variation cache for 22:51000001-52000000
WARNING: Could not find variation cache for 22:51000001-52000000
WARNING: Could not find variation cache for 22:51000001-52000000
WARNING: Could not find cache for 22:51000001-52000000
WARNING: Could not find cache for 22:51000001-52000000

When I checked the actual cache folder, there is no file in such range. Is
this something I should consider or can I ignore this message?

For your information, the vep cahce is downloaded in this location:
ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh38.tar.gz

Thank you very much!
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