<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Now that I have subscribed in Ensemble dev..<br><br>It would be very helpful for me if you check this vep issue with the condel module.<br>
<br>Thanks <br>Treesa Binit<br><br><br><div class="gmail_quote"><div><div class="h5">On Wed, Oct 10, 2012 at 4:29 PM, <span dir="ltr"><<a href="mailto:dev-owner@ensembl.org" target="_blank">dev-owner@ensembl.org</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">The Ensembl dev mailing list only accepts postings from people who are<br>
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<br><br></div></div>---------- Forwarded message ----------<br>From: binit treesa <<a href="mailto:binit.treesa@gmail.com" target="_blank">binit.treesa@gmail.com</a>><br>To: <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
Cc: Neeba Dijo <<a href="mailto:neebasebastian@gmail.com" target="_blank">neebasebastian@gmail.com</a>><br>
Date: Wed, 10 Oct 2012 16:29:35 +0530<br>Subject: VEP run with condel, sift and polyphen options<br>Hi,<br><br>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 . <br>
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.<br>
<br>And I'm confused on the correctness of these calculated score.<br><br>It would be better if you check and comment about the output generated here. <br><br>Details of the <a href="http://vep.pl" target="_blank">vep.pl</a> run is given below<br>
<br><b>Input File :test.txt</b><br><br>#CHROM_ID START ID REF ALT<br>1 94586536 . C A<br>1 94586536 . C G<br><br><br><b>Output file : testOutput.txt</b><br>
<br>## ENSEMBL VARIANT EFFECT PREDICTOR v2.6<br>## Output produced at 2012-10-10 06:37:22<br>## Connected to homo_sapiens_core_68_37 on <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a><br>
## Using API version 68, DB version 68<br>
## Extra column keys:<br>## DISTANCE : Shortest distance from variant to transcript<br>## PolyPhen : PolyPhen prediction<br>## SIFT : SIFT prediction<br>## Condel : Consensus deleteriousness score for an amino acid substitution based on SIFT and PolyPhen-2<br>
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra<br>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)<br>
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)<br>
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)<br>
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)<br>
<br><br><b>Command used</b><br><br>perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i test.txt -o testOutput.txt -sift b -polyphen b -plugin Condel,/users/tbinit/.vep/Plugins/config/Condel/config,b --force<br>
<br><b>The status of the processing is shown </b><br><br>readline() on closed filehandle SIFT at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 136.<br>readline() on closed filehandle POLYPHEN at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 147.<br>
2012-10-10 05:50:00 - Loaded plugin: Condel<br>2012-10-10 05:50:02 - Starting...<br>2012-10-10 05:50:02 - Detected format of input file as vcf<br>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.<br>
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.<br>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.<br>
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.<br>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.<br>
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.<br>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.<br>
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.<br>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.<br>
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.<br>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.<br>
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.<br>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.<br>
WARNING: Start or end -1 coordinate invalid on line 4<br>2012-10-10 05:50:02 - Read 2 variants into buffer<br>2012-10-10 05:50:02 - Skipping 0 non-variant loci<br>2012-10-10 05:50:02 - Reading transcript data from cache and/or database<br>
[================================================================================================================================] [ 100% ]<br>2012-10-10 05:50:06 - Retrieved 9 transcripts (0 mem, 0 cached, 9 DB, 0 duplicates)<br>
2012-10-10 05:50:06 - Analyzing chromosome 1<br>2012-10-10 05:50:06 - Analyzing variants<br>[================================================================================================================================] [ 100% ]<br>
2012-10-10 05:50:08 - Calculating consequences<br>[> ] [ 0% ]Use of uninitialized value in subtraction (-) at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.<br>
Use of uninitialized value in subtraction (-) at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 212, <GEN0> line 4.<br>Use of uninitialized value in subtraction (-) at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.<br>
Use of uninitialized value in subtraction (-) at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 216, <GEN0> line 4.<br>[==============================================================> ] [ 50% ]Use of uninitialized value in subtraction (-) at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.<br>
Use of uninitialized value in subtraction (-) at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 212, <GEN0> line 4.<br>Use of uninitialized value in subtraction (-) at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.<br>
Use of uninitialized value in subtraction (-) at /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 216, <GEN0> line 4.<br>[================================================================================================================================] [ 100% ]<br>
2012-10-10 05:50:11 - Processed 2 total variants (0 vars/sec, 0 vars/sec total)<br>2012-10-10 05:50:11 - Finished!<br><br><br>Thanks<br>Treesa Binit<br>
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