[ensembl-dev] VEP error : 'Can't call method "db" on unblessed reference'
Will McLaren
wm2 at ebi.ac.uk
Tue Mar 4 10:30:44 GMT 2014
Hello Mike,
I have a feeling this is a bug that has already been reported and fixed.
If you update your API install (either using CVS if you did it manually, or
by re-running INSTALL.pl), you should pick up this fix.
Let me know if you still see the problem - I have tested with the updated
code and I don't get the same error.
Regards
Will
On 3 March 2014 12:50, MolOncAdmin <MolOncAdmin at cruk.manchester.ac.uk>wrote:
> 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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