[ensembl-dev] VEP run with condel, sift and polyphen options

Mon Oct 15 12:40:55 BST 2012

Hello again,

I still don't see these errors - perhaps your Condel configuration
file is missing some values?

Also try updating your Condel.pm and config from the GitHub repository again.

Mine looks like:

> cat ~/.vep/Plugins/config/Condel/config/condel_SP.conf
condel.dir='~/.vep/Plugins/config/Condel/'

#------------------------------------------------------------------------------
cutoff.HumVar.sift='0.15'
cutoff.HumVar.polyphen='0.28'
cutoff.HUmVar.condel='0.46'
#------------------------------------------------------------------------------
max.HumVar.sift='1'
max.HumVar.polyphen='1'

On 15 October 2012 11:42, binit treesa <binit.treesa at gmail.com> wrote:
> Will McLaren,
>
> Thanks for spending time on this data.
>
> I rechecked the input data. There are no empty lines.
> And I tried the format option in the VEP command as the input is in vcf
> format.
>
> Command:
>
> perl variant_effect_predictor.pl -i testinput3.vcf -format vcf -o
> outputCondel.txt -sift b -polyphen b  -plugin
> Condel,/users/tbinit/.vep/Plugins/config/Condel/config,b,2
>
> But still I am getting the same output and showing only 50% completeness in
> calculating the consequences.
>
> Here attached the screen shot of VEP run and the output file generated.
> Condel scores are pretty same as previous output.
>
> Can you please check this output (condel score) with the one that your VEP
> run generated with the the same input.
>
> Thanks
> Treesa Binit
>
>
>>
>>
>> ---------- Forwarded message ----------
>> From: binit treesa <binit.treesa at gmail.com>
>> To: dev at ensembl.org
>> Cc: Neeba Dijo <neebasebastian at gmail.com>
>> Date: Wed, 10 Oct 2012 16:29:35 +0530
>> Subject: VEP run with condel, sift and polyphen options
>> Hi,
>>
>> I have downloaded the VEP version 2.6 and tried to run this script with a
>> variant file. It executed succesfully and generated the output file .
>> But when I executed this with the options for "sift, polyphen and condel
>> plugin", it throws some erros. Eventhough it calculated all the score and
>> generated the output file.
>>
>> And I'm confused on the correctness of these calculated score.
>>
>> It would be better if you check and comment about the output generated
>> here.
>>
>> Details of the vep.pl run is given below
>>
>> Input File :test.txt
>>
>> #CHROM_ID       START   ID      REF     ALT
>> 1       94586536        .       C       A
>> 1       94586536        .       C       G
>>
>>
>> Output file : testOutput.txt
>>
>> ## ENSEMBL VARIANT EFFECT PREDICTOR v2.6
>> ## Output produced at 2012-10-10 06:37:22
>> ## Connected to homo_sapiens_core_68_37 on ensembldb.ensembl.org
>> ## Using API version 68, DB version 68
>> ## Extra column keys:
>> ## DISTANCE : Shortest distance from variant to transcript
>> ## PolyPhen : PolyPhen prediction
>> ## SIFT : SIFT prediction
>> ## Condel    : Consensus deleteriousness score for an amino acid
>> substitution based on SIFT and PolyPhen-2
>> #Uploaded_variation    Location    Allele    Gene    Feature
>> Feature_type    Consequence    cDNA_position    CDS_position
>> Protein_position    Amino_acids    Codons    Existing_variation    Extra
>> 1_94586536_C/A    1:94586536    A    ENSG00000198691    ENST00000370225
>> Transcript    missense_variant,splice_region_variant    153    66    22
>> K/N    aaG/aaT    -
>> PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.885);SIFT=tolerated(0.09)
>> 1_94586536_C/A    1:94586536    A    ENSG00000198691    ENST00000535735
>> Transcript    missense_variant,splice_region_variant    146    66    22
>> K/N    aaG/aaT    -
>> PolyPhen=benign(0.235);Condel=deleterious(0.583);SIFT=tolerated(0.07)
>> 1_94586536_C/G    1:94586536    G    ENSG00000198691    ENST00000370225
>> Transcript    missense_variant,splice_region_variant    153    66    22
>> K/N    aaG/aaC    -
>> PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.885);SIFT=tolerated(0.09)
>> 1_94586536_C/G    1:94586536    G    ENSG00000198691    ENST00000535735
>> Transcript    missense_variant,splice_region_variant    146    66    22
>> K/N    aaG/aaC    -
>> PolyPhen=benign(0.235);Condel=deleterious(0.583);SIFT=tolerated(0.07)
>>
>>
>> Command used
>>
>> perl variant_effect_predictor.pl -i test.txt -o testOutput.txt -sift b
>> -polyphen b  -plugin
>> Condel,/users/tbinit/.vep/Plugins/config/Condel/config,b --force
>>
>> The status of the processing is shown
>>
>> readline() on closed filehandle SIFT at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 136.
>> readline() on closed filehandle POLYPHEN at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 147.
>> 2012-10-10 05:50:00 - Loaded plugin: Condel
>> 2012-10-10 05:50:02 - Starting...
>> 2012-10-10 05:50:02 - Detected format of input file as vcf
>> Use of uninitialized value $data[4] in string eq at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 316, <GEN0> line 4.
>> Use of uninitialized value $ref in length at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 349, <GEN0> line 4.
>> Use of uninitialized value $alt in pattern match (m//) at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 352, <GEN0> line 4.
>> Use of uninitialized value $alt in split at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 425, <GEN0> line 4.
>> Use of uninitialized value $alt in pattern match (m//) at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 434, <GEN0> line 4.
>> Use of uninitialized value $ref in concatenation (.) or string at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 501, <GEN0> line 4.
>> Use of uninitialized value $alt in concatenation (.) or string at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 501, <GEN0> line 4.
>> Use of uninitialized value $data[2] in string eq at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 501, <GEN0> line 4.
>> Use of uninitialized value in pattern match (m//) at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 1944, <GEN0> line 4.
>> Use of uninitialized value in substitution (s///) at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 1944, <GEN0> line 4.
>> Use of uninitialized value in string eq at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 1945, <GEN0> line 4.
>> Use of uninitialized value in pattern match (m//) at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 1950, <GEN0> line 4.
>> Use of uninitialized value in concatenation (.) or string at
>> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 1951, <GEN0> line 4.
>> WARNING: Start  or end -1 coordinate invalid on line 4
>> 2012-10-10 05:50:02 - Read 2 variants into buffer
>> 2012-10-10 05:50:02 - Skipping 0 non-variant loci
>> 2012-10-10 05:50:02 - Reading transcript data from cache and/or database
>>
>> [================================================================================================================================]
>> [ 100% ]
>> 2012-10-10 05:50:06 - Retrieved 9 transcripts (0 mem, 0 cached, 9 DB, 0
>> duplicates)
>> 2012-10-10 05:50:06 - Analyzing chromosome 1
>> 2012-10-10 05:50:06 - Analyzing variants
>>
>> [================================================================================================================================]
>> [ 100% ]
>> 2012-10-10 05:50:08 - Calculating consequences
>> [>
>> ]    [ 0% ]Use of uninitialized value in subtraction (-) at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.
>> Use of uninitialized value in subtraction (-) at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 212, <GEN0> line 4.
>> Use of uninitialized value in subtraction (-) at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.
>> Use of uninitialized value in subtraction (-) at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 216, <GEN0> line 4.
>> [==============================================================>
>> ]   [ 50% ]Use of uninitialized value in subtraction (-) at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.
>> Use of uninitialized value in subtraction (-) at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 212, <GEN0> line 4.
>> Use of uninitialized value in subtraction (-) at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.
>> Use of uninitialized value in subtraction (-) at
>> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 216, <GEN0> line 4.
>>
>> [================================================================================================================================]
>> [ 100% ]
>> 2012-10-10 05:50:11 - Processed 2 total variants (0 vars/sec, 0 vars/sec
>> total)
>> 2012-10-10 05:50:11 - Finished!
>>
>>
>> Thanks
>> Treesa Binit
>>
>
>