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

[Graham Ritchie]

Hi Michael,

This bug occurs because a motif feature from the regulation database somehow does not have an associated binding matrix. This should not happen, and we think this is a data bug in the regulation databases and we are looking into it. In the mean time though I have committed a fix to the release 65 branch for the VEP which works around this by simply ignoring such anomalous motif features, so if you can redownload it or update your copy of the code you should be able to continue your analysis.

Let us know if you encounter any further problems.

Cheers,

Graham


On 18 Dec 2011, at 19:02, Michael Yourshaw wrote:

> 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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