[ensembl-dev] VEP run with condel, sift and polyphen options
Will McLaren
wm2 at ebi.ac.uk
Fri Oct 12 10:30:05 BST 2012
Hello,
I think there may be some issue with your input file - are there any
empty or malformed lines in it, or perhaps you have none-standard line
termination characters (this can happen if the file is generated on a
Windows machine)?
If I copy and paste just the input lines to a test file from your
email I don't see any errors with the Condel plugin.
Regards
Will McLaren
Ensembl Variation
On 12 October 2012 05:45, binit treesa <binit.treesa at gmail.com> wrote:
>> Now that I have subscribed in Ensemble dev..
>>
>> It would be very helpful for me if you check this vep issue with the
>> condel module.
>>
>> Thanks
>> Treesa Binit
>>
>>
>> On Wed, Oct 10, 2012 at 4:29 PM, <dev-owner at ensembl.org> wrote:
>>>
>>> The Ensembl dev mailing list only accepts postings from people who are
>>> subscribed. You can subscribe or unsubscribe at
>>> http://lists.ensembl.org/mailman/listinfo/dev
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>>>
>>>
>>> ---------- 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
>>>
>>
>
>
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