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

Tue Mar 4 12:03:14 GMT 2014

Hi Will,

Yes removing the polyphen option fixed it. Thanks a lot. I thought it was available along with SIFT for the mice after version 71, my mistake.
I guess the reason the other vcf with the coordinates from assem.37 was working fine is because the SNVs wasn’t falling in protein coding regions, is that right?

Thanks again and thanks for developing the VEP, its a vary nice tool!

Mike

From: Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Tuesday, 4 March 2014 10:33
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] VEP error : 'Can't call method "db" on unblessed reference'

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<mailto: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<mailto: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<tel:6%20108505905> . T C . . .
6 115968860 . G A . . .
6 118413764 . A C . . .
6 130062085 . G T . . .
6 130185532 . C G . . .
1 146831660 . G A . . .
6 146861758<tel:6%20146861758> . T C . . .

file coor. assem. 37;

1 14221605 . T C .
1 148678790 . G A .
6 83212439 . A G .
6 108455899<tel:6%20108455899> . T C .
6 115918878 . G A .
6 118363782 . A C .
6 130012103 . G T .
6 130135550 . C G .
6 146810280<tel:6%20146810280> . 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<http://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<mailto: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<http://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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This email is confidential and intended solely for the use of the person(s) ('the intended recipient') to whom it was addressed. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Cancer Research UK Manchester Institute or the University of Manchester. It may contain information that is privileged & confidential within the meaning of applicable law. Accordingly any dissemination, distribution, copying, or other use of this message, or any of its contents, by any person other than the intended recipient may constitute a breach of civil or criminal law and is strictly prohibited. If you are NOT the intended recipient please contact the sender and dispose of this e-mail as soon as possible.