search

bahlolab / PLASTER

Nextflow pipeline for long amplicon typing of PacBio SMRT sequencing data
MIT License
2 stars 3 forks source link

Change Ensembl API Version #16

Closed cyriltata closed 2 years ago

cyriltata commented 2 years ago

Where can one change the ensembl api version? I get this error because my DB is 106. Tried on this line https://github.com/bahlolab/PLASTER/blob/master/test/typing.config#L7 with no success

Command error:
  Possible precedence issue with control flow operator at /opt/conda/envs/PLASTER_22.05.01/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

  -------------------- WARNING ----------------------
  MSG: homo_sapiens is not a valid species name (check DB and API version)
  FILE: Bio/EnsEMBL/Registry.pm LINE: 1334
  CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 1109
  Date (localtime)    = Sat May 28 16:27:45 2022
  Ensembl API version = 104
  ---------------------------------------------------
jemunro commented 2 years ago

It's probably because the version of ensemble-vep installed in docker container is 104, and is not compatible with future database versions. The easiest solution would be for you to download vep cache GRCh38 version 104 from http://ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_vep_104_GRCh38.tar.gz, see https://ensembl.org/info/docs/tools/vep/script/vep_cache.html

cyriltata commented 2 years ago

@jemunro downgraded the database and it worked