[ensembl-dev] CONDEL plugin bug?

Graham Ritchie grsr at ebi.ac.uk
Thu May 10 15:00:08 BST 2012


Hi Duarte,

Have you set the 'condel.dir' parameter in the config/Condel/config/condel_SP.conf file to the correct full path to the config/Condel/ directory on your system? I know the configuration for this plugin is a bit fiddly, but we have tried to stick to the way that the standalone version of Condel is distributed.

I will add a bit more error checking to the script to help debug this as well.

Cheers,

Graham


On 10 May 2012, at 14:44, Duarte Molha wrote:

> Dear developers
>  
> I have downloaded the latest VEP and tried to run the example file though it using the condel script and I am getting some error messages:
>  
> Here is the Error output:
>  
> Command Used:
>  
> perl variant_effect_predictor.pl -i example.vcf --dir /ReferenceData/vep_cache/ --plugin Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b --force --sift b --polyphen b –verbose
>  
> OUTPUT:
>  
> #----------------------------------#
> # ENSEMBL VARIANT EFFECT PREDICTOR #
> #----------------------------------#
>  
> version 2.5
>  
> By Will McLaren (wm2 at ebi.ac.uk)
>  
> Configuration options:
>  
> core_type          core
> dir                /ReferenceData/vep_cache/
> force_overwrite    1
> host               ensembldb.ensembl.org
> input_file         example.vcf
> plugin             Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b
> polyphen           b
> port               5306
> sift               b
> species            homo_sapiens
> toplevel_dir       /ReferenceData/vep_cache/
> verbose            1
>  
> --------------------
>  
> Will only load v67 databases
> Species 'homo_sapiens' loaded from database 'homo_sapiens_core_67_37'
> Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_67_37'
> Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_67_37'
> Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_67_37'
> Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_67_37'
> homo_sapiens_variation_67_37 loaded
> homo_sapiens_funcgen_67_37 loaded
> Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so the following compara databases will be ignored: ensembl_compara_67
> ensembl_ancestral_67 loaded
> ensembl_ontology_67 loaded
> 2012-05-10 14:39:32 - Connected to core version 67 database and variation version 67 database
> readline() on closed filehandle SIFT at /ReferenceData/vep_cache//Plugins/Condel.pm line 136.
> readline() on closed filehandle POLYPHEN at /ReferenceData/vep_cache//Plugins/Condel.pm line 147.
> 2012-05-10 14:39:32 - Loaded plugin: Condel
> 2012-05-10 14:39:33 - Starting...
> 2012-05-10 14:39:33 - Detected format of input file as vcf
> 2012-05-10 14:39:33 - Read 173 variants into buffer
> 2012-05-10 14:39:33 - Analyzing chromosome 21
> 2012-05-10 14:39:33 - Reading transcript data from cache and/or database
> [====================================================================================================================================================================]  [ 100% ]
> 2012-05-10 14:40:02 - Retrieved 132 transcripts (0 mem, 0 cached, 217 DB, 85 duplicates)
> 2012-05-10 14:40:02 - Analyzing variants
> [====================================================================================================================================================================]  [ 100% ]
> 2012-05-10 14:40:40 - Calculating and writing output
> [>                                                                                                                                                                   ]    [ 0% ]Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 203, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> [=============================>                                                                                                                                      ]   [ 18% ]Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 203, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 212, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 203, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 212, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 203, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 212, <GEN0> line 175.
> [=================================>                                                                                                                                  ]   [ 21% ]Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> [==========================================>                                                                                                                         ]   [ 27% ]Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.
> Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.
> [===============================================>  
> ....
>  
> Can you tell be it there is something wrong with my command line arguments? Or I should just  ignore these warining messages?
>  
> Best regards                                                          
>  
> Duarte Molha
> 
> Computational Biologist
> Oxford Gene Technology
> Begbroke Science Park
> Sandy Lane Yarnton
> Oxford OX5 1PF UK
> 
> T: +44 (0)1865 856 837
> F: +44 (0)1865 842 116
> C: +44 (0)7772 111 304
> E: duarte.molha at ogt.co.uk
> W: www.ogt.co.uk
>  
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