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

Tue Mar 4 10:33:03 GMT 2014

Hello again,

Sorry, my mistake, missed the obvious!

You are using --polyphen; this option is not available for mouse (it is a
human-specific algorithm) and is causing the error. If you remove that it
should work fine.

Regards

Will

On 4 March 2014 10:30, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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