[ensembl-dev] VEP error “No sequence_level coord_system is defined”

[Michael Yourshaw]

In VEP version 75 I'm getting the warning "uninitialized value $version” followed by the error “No sequence_level coord_system is defined”).

Might there be something wrong with my setup, which consists of a local db installation and the downloaded cache?

Full transcript follows.

2014-08-09 17:18:51 - Read configuration from /home/myourshaw/lab/pypeline/vax/75/vep_no_plugins.ini
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

version 75

By Will McLaren (wm2 at ebi.ac.uk)

Configuration options:

allele_number      1
biotype            1
cache              1
canonical          1
ccds               1
check_alleles      1
check_existing     1
check_ref          1
check_svs          1
config             /home/myourshaw/lab/pypeline/vax/75/vep_no_plugins.ini
core_type          core
database           1
dir                /share/apps/myourshaw/vax/vep_cache
dir_cache          /share/apps/myourshaw/vax/vep_cache
dir_plugins        /share/apps/myourshaw/vax/Plugins
domains            1
force_overwrite    1
gene               1
gmaf               1
hgvs               1
host               cortex.local
input_file         /scratch1/tmp/myourshaw/rnaseq_20140227/vcfs/gatk/rnaseq_20140227.hc.analysis_ready.vcf
maf_1kg            1
maf_esp            1
no_progress        1
numbers            1
output_file        /scratch1/tmp/myourshaw/rnaseq_20140227/vcfs/gatk/rnaseq_20140227.hc.analysis_ready.vcf.vax
password           xxx
polyphen           b
port               3306
protein            1
pubmed             1
regulatory         1
sift               b
species            homo_sapiens
stats              HASH(0x6665860)
symbol             1
terms              SO
user               xxx
verbose            1
xref_refseq        0

--------------------

Will only load v75 databases
Species 'homo_sapiens' loaded from database 'homo_sapiens_core_75_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_75_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_75_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_75_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_75_37'
homo_sapiens_variation_75_37 loaded
homo_sapiens_funcgen_75_37 loaded
ensembl_compara_75 loaded
ensembl_ancestral_75 loaded
ensembl_ontology_75 loaded
No production database or adaptor found
ensembl_stable_ids_75 loaded
2014-08-09 17:19:18 - Connected to core version 75 database and variation version 75 database
2014-08-09 17:19:18 - Read existing cache info
Use of uninitialized value $version in concatenation (.) or string at /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm line 304.
Use of uninitialized value $version in concatenation (.) or string at /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm line 304.
Use of uninitialized value $version in concatenation (.) or string at /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm line 304.
Use of uninitialized value $version in concatenation (.) or string at /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm line 304.
Use of uninitialized value $version in concatenation (.) or string at /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm line 304.
Use of uninitialized value $version in concatenation (.) or string at /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm line 304.
2014-08-09 17:22:42 - INFO: Database will be accessed when using --hgvs
2014-08-09 17:22:42 - INFO: Database will be accessed when using --check_ref
2014-08-09 17:22:42 - Starting...
2014-08-09 17:22:42 - Detected format of input file as vcf

-------------------- EXCEPTION --------------------
MSG: No sequence_level coord_system is defined
STACK Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_sequence_level /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm:631
STACK Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_Slice_start_end_strand /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm:246
STACK Bio::EnsEMBL::Slice::seq /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/Slice.pm:655
STACK Bio::EnsEMBL::Variation::Utils::VEP::validate_vf /share/apps/myourshaw/vax/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:2844
STACK main::main /home/myourshaw/lab/pypeline/vax/vep.pl:289
STACK toplevel /home/myourshaw/lab/pypeline/vax/vep.pl:172
Date (localtime)    = Sat Aug  9 17:23:17 2014
Ensembl API version = 75
---------------------------------------------------


ॐ

Michael Yourshaw, PhD
UCLA Geffen School of Medicine
Department of Pediatrics
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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