<div dir="ltr">Hello Mike,<div><br></div><div>I have a feeling this is a bug that has already been reported and fixed.</div><div><br></div><div>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.</div>
<div><br></div><div>Let me know if you still see the problem - I have tested with the updated code and I don't get the same error.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 3 March 2014 12:50, MolOncAdmin <span dir="ltr"><<a href="mailto:MolOncAdmin@cruk.manchester.ac.uk" target="_blank">MolOncAdmin@cruk.manchester.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear VEP developers,<br>
<br>
I have difficulties running the VEP version 73 with mouse vcf files with coordinates of assembly 38 (mm10).<br>
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."<br>
Although, if I run the same script with vcfs with coordinates of assembly 37 (mm9) it runs fine.<br>
See the script and files below.<br>
<br>
Any help is greatly appreciated.<br>
<br>
Kind regards,<br>
<br>
Mike Gavrielides | Bioinformatician, Software developer<br>
Molecular Oncology Group<br>
Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX<br>
<br>
<br>
file with coor. assem. 38 '1906.snp.cand.snvs.pass.thresh.vcf.38', (throughs the error):<br>
<br>
##fileformat=VCFv4.1<br>
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"><br>
##INFO=<ID=H2,Number=0,Type=Flag,Description="Hapmap2 Membership"><br>
##INFO=<ID=H3,Number=0,Type=Flag,Description="Hapmap3 Membership"><br>
##INFO=<ID=RL,Number=1,Type=String,Description="Resource Link"><br>
##INFO=<ID=FBV,Number=1,Type=String,Description="Frequency Based Validation"><br>
##INFO=<ID=GTP,Number=1,Type=String,Description="Genotype"><br>
##INFO=<ID=QC,Number=1,Type=String,Description="Quality Check"><br>
#CHROM POS ID REF ALT QUAL FILTER INFO<br>
1 14231524 . T C . . .<br>
19 29067507 . C T . . .<br>
9 37537480 . C T . . .<br>
15 73792647 . C T . . .<br>
6 83262445 . A G . . .<br>
6 108505905 . T C . . .<br>
6 115968860 . G A . . .<br>
6 118413764 . A C . . .<br>
6 130062085 . G T . . .<br>
6 130185532 . C G . . .<br>
1 146831660 . G A . . .<br>
6 146861758 . T C . . .<br>
<br>
file coor. assem. 37;<br>
<br>
1 14221605 . T C .<br>
1 148678790 . G A .<br>
6 83212439 . A G .<br>
6 108455899 . T C .<br>
6 115918878 . G A .<br>
6 118363782 . A C .<br>
6 130012103 . G T .<br>
6 130135550 . C G .<br>
6 146810280 . T C .<br>
9 37345065 . C T .<br>
15 73623077 . C T .<br>
19 29141997 . C T .<br>
<br>
script:<br>
perl /opt/gridware/pkg/apps/ensemblvep/73/linux-x86_64/bin/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> \<br>
-i /groups/mnt1/molecularoncology/vcfs/test/1906.snp.cand.snvs.pass.thresh.vcf.38 \<br>
-o /groups/mnt1/molecularoncology/vcfs/test/1906.snp.cand.snvs.pass.thresh.vep.38 \<br>
--offline \<br>
--species mus_musculus \<br>
--sift s \<br>
--polyphen s \<br>
--regulatory \<br>
--symbol \<br>
--domains \<br>
--ccds \<br>
--gmaf \<br>
--check_existing \<br>
--check_alleles \<br>
--no_progress \<br>
--verbose \<br>
--cache \<br>
--dir /groups/mnt1/molecularoncology/mks/VEPcacheAll/VEPcacheMM.73<br>
<br>
Output:<br>
<br>
#----------------------------------#<br>
# ENSEMBL VARIANT EFFECT PREDICTOR #<br>
#----------------------------------#<br>
<br>
version 73<br>
<br>
By Will McLaren (<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)<br>
<br>
Configuration options:<br>
<br>
cache 1<br>
ccds 1<br>
check_alleles 1<br>
check_existing 1<br>
core_type core<br>
dir /groups/mnt1/molecularoncology/mks/VEPcacheAll/VEPcacheMM.73<br>
dir_plugins /groups/mnt1/molecularoncology/mks/VEPcacheAll/VEPcacheMM.73/Plugins<br>
domains 1<br>
gmaf 1<br>
host <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a><br>
input_file /groups/mnt1/molecularoncology/vcfs/test/1906.snp.cand.snvs.pass.thresh.vcf.38<br>
no_progress 1<br>
offline 1<br>
output_file /groups/mnt1/molecularoncology/vcfs/test/1906.snp.cand.snvs.pass.thresh.vep.38<br>
polyphen s<br>
port 5306<br>
regulatory 1<br>
sift s<br>
species mus_musculus<br>
stats HASH(0x1bdfb68)<br>
symbol 1<br>
verbose 1<br>
<br>
--------------------<br>
<br>
2014-03-03 12:25:03 - Read existing cache info<br>
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)<br>
2014-03-03 12:25:03 - Starting...<br>
2014-03-03 12:25:03 - Detected format of input file as vcf<br>
2014-03-03 12:25:03 - Read 12 variants into buffer<br>
2014-03-03 12:25:03 - Reading transcript data from cache and/or database<br>
2014-03-03 12:25:04 - Retrieved 538 transcripts (0 mem, 538 cached, 0 DB, 0 duplicates)<br>
2014-03-03 12:25:04 - Reading regulatory data from cache and/or database<br>
2014-03-03 12:25:04 - Retrieved 2068 regulatory features (0 mem, 2068 cached, 0 DB, 0 duplicates)<br>
2014-03-03 12:25:04 - Checking for existing variations<br>
2014-03-03 12:25:11 - Analyzing chromosome 1<br>
2014-03-03 12:25:11 - Analyzing variants<br>
2014-03-03 12:25:11 - Analyzing RegulatoryFeatures<br>
2014-03-03 12:25:11 - Analyzing MotifFeatures<br>
2014-03-03 12:25:11 - Calculating consequences<br>
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.<br>
<br>
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</blockquote></div><br></div>