[ensembl-dev] vep 2.3 issues

[Hardip Patel]

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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