[ensembl-dev] VEP error : 'Can't call method "db" on unblessed reference'

[MolOncAdmin]

Dear VEP developers,

I have difficulties running the VEP version 73 with mouse vcf files with coordinates of assembly 38 (mm10).
During the step "Calculating consequences" it throughs the error: "Can't call method "db" on unblessed reference at /opt/gridware/pkg/apps/ensemblvep/73/linux-x86_64/perl/lib/perl5/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 313."
Although, if I run the same script with vcfs with coordinates of assembly 37 (mm9) it runs fine.
See the script and files below.

Any help is greatly appreciated.

Kind regards,

Mike Gavrielides  |  Bioinformatician, Software developer
Molecular Oncology Group
Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX


file with coor. assem. 38 '1906.snp.cand.snvs.pass.thresh.vcf.38', (throughs the error):

##fileformat=VCFv4.1
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=H2,Number=0,Type=Flag,Description="Hapmap2 Membership">
##INFO=<ID=H3,Number=0,Type=Flag,Description="Hapmap3 Membership">
##INFO=<ID=RL,Number=1,Type=String,Description="Resource Link">
##INFO=<ID=FBV,Number=1,Type=String,Description="Frequency Based Validation">
##INFO=<ID=GTP,Number=1,Type=String,Description="Genotype">
##INFO=<ID=QC,Number=1,Type=String,Description="Quality Check">
#CHROM POS ID REF ALT QUAL FILTER INFO
1 14231524 . T C . . .
19 29067507 . C T . . .
9 37537480 . C T . . .
15 73792647 . C T . . .
6 83262445 . A G . . .
6 108505905 . T C . . .
6 115968860 . G A . . .
6 118413764 . A C . . .
6 130062085 . G T . . .
6 130185532 . C G . . .
1 146831660 . G A . . .
6 146861758 . T C . . .

file coor. assem. 37;

1 14221605 . T C .
1 148678790 . G A .
6 83212439 . A G .
6 108455899 . T C .
6 115918878 . G A .
6 118363782 . A C .
6 130012103 . G T .
6 130135550 . C G .
6 146810280 . T C .
9 37345065 . C T .
15 73623077 . C T .
19 29141997 . C T .

script:
        perl /opt/gridware/pkg/apps/ensemblvep/73/linux-x86_64/bin/variant_effect_predictor.pl \
         -i /groups/mnt1/molecularoncology/vcfs/test/1906.snp.cand.snvs.pass.thresh.vcf.38 \
         -o /groups/mnt1/molecularoncology/vcfs/test/1906.snp.cand.snvs.pass.thresh.vep.38 \
         --offline \
         --species mus_musculus \
         --sift s \
         --polyphen s \
         --regulatory \
         --symbol \
         --domains  \
         --ccds \
         --gmaf \
         --check_existing \
         --check_alleles \
         --no_progress \
         --verbose \
         --cache \
         --dir /groups/mnt1/molecularoncology/mks/VEPcacheAll/VEPcacheMM.73

Output:

#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

version 73

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

Configuration options:

cache             1
ccds              1
check_alleles     1
check_existing    1
core_type         core
dir               /groups/mnt1/molecularoncology/mks/VEPcacheAll/VEPcacheMM.73
dir_plugins       /groups/mnt1/molecularoncology/mks/VEPcacheAll/VEPcacheMM.73/Plugins
domains           1
gmaf              1
host              ensembldb.ensembl.org
input_file        /groups/mnt1/molecularoncology/vcfs/test/1906.snp.cand.snvs.pass.thresh.vcf.38
no_progress       1
offline           1
output_file       /groups/mnt1/molecularoncology/vcfs/test/1906.snp.cand.snvs.pass.thresh.vep.38
polyphen          s
port              5306
regulatory        1
sift              s
species           mus_musculus
stats             HASH(0x1bdfb68)
symbol            1
verbose           1

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

2014-03-03 12:25:03 - Read existing cache info
2014-03-03 12:25:03 - INFO: Database will be accessed when using --polyphen; consider using the complete cache containing polyphen data (see documentation for details)
2014-03-03 12:25:03 - Starting...
2014-03-03 12:25:03 - Detected format of input file as vcf
2014-03-03 12:25:03 - Read 12 variants into buffer
2014-03-03 12:25:03 - Reading transcript data from cache and/or database
2014-03-03 12:25:04 - Retrieved 538 transcripts (0 mem, 538 cached, 0 DB, 0 duplicates)
2014-03-03 12:25:04 - Reading regulatory data from cache and/or database
2014-03-03 12:25:04 - Retrieved 2068 regulatory features (0 mem, 2068 cached, 0 DB, 0 duplicates)
2014-03-03 12:25:04 - Checking for existing variations
2014-03-03 12:25:11 - Analyzing chromosome 1
2014-03-03 12:25:11 - Analyzing variants
2014-03-03 12:25:11 - Analyzing RegulatoryFeatures
2014-03-03 12:25:11 - Analyzing MotifFeatures
2014-03-03 12:25:11 - Calculating consequences
Can't call method "db" on unblessed reference at /opt/gridware/pkg/apps/ensemblvep/73/linux-x86_64/perl/lib/perl5/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 313.

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