[ensembl-dev] CONDEL plugin bug?
Duarte Molha
Duarte.Molha at ogt.co.uk
Thu May 10 14:44:41 BST 2012
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<mailto:duarte.molha at ogt.co.uk>
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