[ensembl-dev] vep 2.3 issues

[Will McLaren]

Hi Hardip,

Is there a reason why you are specifying the cache AND a local
database? Using the options below you shouldn't need the database as
well.

This error is raised because the script can't get a slice adaptor for
your database. This might be for a number of reasons - have you
generated the cache yourself, or downloaded it from our website? If
you have downloaded it, I am surprised that you are getting the line:

2012-01-27 10:41:59 - Reading cached adaptor data

in your output.

You could try deleting (or simply renaming for a backup) the
adaptors.gz file in ~/.vep/homo_sapiens/65/ - this should force the
script to reload the database adaptors on startup and may solve the
problem.

It is odd that it doesn't work for those two chromosomes! Both files
work fine for me, using either cache or database. However, a quick
look on Ensembl shows you're not missing much, at least for your chr15
file:

http://www.ensembl.org/Homo_sapiens/Location/View?r=15%3A20000447-20014544

(this is the range of the chromosome covered by the variants in that file).

Hope this helps

Will

On 27 January 2012 03:50, Hardip Patel <hardip.patel at anu.edu.au> wrote:
> Dear all
>
> I am trying to run the following command for using VEP. I am running local
> version of the ensembl database (v65). I am using perl version 5.14.2.
>
> perl5.14.2 variant_effect_predictor.pl --output_file outfile.vep --species
> homo_sapiens --host host --user user --password password --port 1111
> --db_version 65 --format vcf --buffer 1000000000 --terms ensembl --canonical
> --hgnc --cache --regulatory --protein --gene --condel b --polyphen b --sift
> b --force_overwrite --input_file infile.vcf -skip_db_check
>
> I have VCF files generated for all chromosomes separately for 15 samples.
> The script works all good for all chromosomes for all samples except for
> chr14 and chr15.
>
> Here is the log report after trying to run the script for chr14 and chr15.
>
> Use of qw(...) as parentheses is deprecated at variant_effect_predictor.pl
> line 848.
> 2012-01-27 10:41:59 - Read existing cache info
> 2012-01-27 10:41:59 - Reading cached adaptor data
> Use of uninitialized value $_[3] in join or string at
> ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 3497.
> 2012-01-27 10:41:59 - INFO: Defined host ##### is different from cached
> 2012-01-27 10:41:59 - Starting...
> 2012-01-27 10:42:03 - Read 131269 variants into buffer
> 2012-01-27 10:42:04 - Analyzing chromosome 14
> 2012-01-27 10:42:04 - Reading transcript data from cache and/or database
> [>                                              ]    [ 0% ]
> Can't call method "fetch_by_region" on unblessed reference at
> ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 2144, <GEN0> line 131296.
>
> I have tried downloading the cache again and see if that helps. However, I
> am not able to run it on these two chromosomes at all. Could you please let
> me know how to correct this issue?
>
> I have attached two vcf files as examples to test the code on your end.
>
> NB: it is the chromosome 14 and 15 that are the issue. rest are all fine and
> giving appropriate results.
>
>
> Any help is greatly appreciated.
>
> Kind regards
>
>
>
>
> Hardip R. Patel, PhD
> Post-doctoral Research Fellow
>
> Genome Discovery Unit and RNA Biology Lab
> Genome Biology Department
> The John Curtin School of Medical Research
> College of Medicine, Biology and Environment
> The Australian National University
> Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia
> Email: hardip.patel at anu.edu.au, patelhardip at gmail.com
> Phone Number: (+61) 0449 180 715
>
>
>
>
>
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