[ensembl-dev] CONDEL plugin bug?
Duarte Molha
Duarte.Molha at ogt.co.uk
Thu May 10 14:55:17 BST 2012
Apologies...
Just realized I had to change the Condel config file to add the correct path to condel.dir (first line of the Condel config file)
Maybe this could be useful information to other users...
Do not forget to update the path on the condel config file within your plugin folder to reflect its location...
In my case :
Edit the file:
/ReferenceData/vep_cache/Plugins/config/Condel/config/condel_SP.conf'
Change the the first line to the condel config folder location:
condel.dir='/ReferenceData/vep_cache/Plugins/config/Condel'
Best regards
Duarte
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Duarte Molha
Sent: 10 May 2012 14:45
To: Ensembl developers list
Subject: [ensembl-dev] CONDEL plugin bug?
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<mailto: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<mailto:duarte.molha at ogt.co.uk>
W: www.ogt.co.uk<http://www.ogt.co.uk/>
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