[ensembl-dev] VEP Can't call method "description" on an undefined value

[Michael Yourshaw]

Variant Effect Predictor error: Can't call method "description" on an undefined value at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 910, <GEN1> line 205.

VEP 2.3
local copy of database v 65

input VCF:
$vf->{_line} = 
1	226497256	TF_binding_site_variant	G	A	.	.	.

VEP.pm line 910:
            my $matrix = $mf->binding_matrix->description.' '.$mf->display_label;

$mf = Bio::EnsEMBL::Variation::MotifFeature
$mf->{binding_matrix} = undef
$mf->{dbID} = 625091
$mf->{display_label} = Gapb:PB0124.1
$mf->{end} = 226497270
$mf->{interdb_stable_id} = undef
$mf->{score} = 0.898
$mf->{slice} = Bio::EnsEMBL::Slice
$mf->{start} = 226497255
$mf->{strand} = −1

STDOUT/STDERR:
Use of qw(...) as parentheses is deprecated at /home/myourshaw/lab/pypeline/vax23/vax23.pl line 852.
2011-12-18 10:35:24 - Reading configuration from /home/myourshaw/lab/pypeline/vax23/vep.ini
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

version 2.3

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

Configuration options:

                   
canonical          1
check_ref          1
condel             b
config             /home/myourshaw/lab/pypeline/vax23/vep.ini
core_type          core
dir                /home/myourshaw/.vep
force_overwrite    1
format             vcf
gene               1
hgnc               1
hgvs               1
host               cortex.local
input_file         /home/myourshaw/lab/pypeline/vax23/snp_test.vcf
no_progress        1
output_file        /home/myourshaw/lab/pypeline/vax23/snp_test.vcf.vax
password           ?
polyphen           b
port               3306
protein            1
regulatory         1
sift               b
species            human
terms              SO
user               ?
verbose            1

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

Will only load v65 databases
Species 'homo_sapiens' loaded from database 'homo_sapiens_core_65_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_65_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_65_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_65_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_65_37'
homo_sapiens_variation_65_37 loaded
homo_sapiens_funcgen_65_37 loaded
ensembl_compara_65 loaded
ensembl_ancestral_65 loaded
ensembl_ontology_65 loaded
2011-12-18 10:35:24 - Connected to core version 65 database and variation version 65 database
2011-12-18 10:35:24 - Starting...
2011-12-18 10:35:27 - Read 204 variants into buffer
2011-12-18 10:35:27 - Analyzing chromosome 1
2011-12-18 10:35:27 - Reading transcript data from cache and/or database
2011-12-18 10:35:29 - Retrieved 449 transcripts (0 mem, 0 cached, 460 DB, 11 duplicates)
2011-12-18 10:35:29 - Analyzing variants
2011-12-18 10:35:36 - Reading regulatory data from cache and/or database
2011-12-18 10:35:38 - Retrieved 208 regulatory features (0 mem, 0 cached, 208 DB, 0 duplicates)
2011-12-18 10:35:38 - Analyzing RegulatoryFeatures
2011-12-18 10:35:38 - Analyzing MotifFeatures
2011-12-18 10:35:38 - Calculating and writing output
Can't call method "description" on an undefined value at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 910, <GEN1> line 205.



ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
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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