Thank you so much Will McLaren !!<br><br>I compared output with yours. It shows difference in the condel score. For previous run, I missed to copy methdist files (<a href="https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel/methdist">https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel/methdist</a>) in the config folder and this caused the errors.<br>
<br>Now that, the errors are resolved completely. I'm getting the output same as yours :)<br><br>Thank you once again<br>Binit<br><br><div class="gmail_quote">On Tue, Oct 16, 2012 at 6:33 PM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<br>
<br>
I think my output looks the same as yours. Output on STDOUT:<br>
<br>
perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i binit.txt -force -sift b -poly b<br>
-plugin Condel,[hidden]/Plugins/config/Condel/config,b<br>
2012-10-15 12:33:21 - Loaded plugin: Condel<br>
2012-10-15 12:33:21 - Starting...<br>
2012-10-15 12:33:21 - Detected format of input file as vcf<br>
2012-10-15 12:33:21 - Read 2 variants into buffer<br>
2012-10-15 12:33:21 - Skipping 0 non-variant loci<br>
2012-10-15 12:33:21 - Reading transcript data from cache and/or database<br>
[==========================================================================================================]<br>
[ 100% ]<br>
2012-10-15 12:33:22 - Retrieved 9 transcripts (0 mem, 0 cached, 9 DB,<br>
0 duplicates)<br>
2012-10-15 12:33:22 - Analyzing chromosome 1<br>
2012-10-15 12:33:22 - Analyzing variants<br>
[==========================================================================================================]<br>
[ 100% ]<br>
2012-10-15 12:33:22 - Calculating consequences<br>
[==========================================================================================================]<br>
[ 100% ]<br>
2012-10-15 12:33:22 - Processed 2 total variants (2 vars/sec, 2 vars/sec total)<br>
2012-10-15 12:33:22 - Finished!<br>
<br>
Output in variant_effect_output.txt:<br>
<div><br>
## ENSEMBL VARIANT EFFECT PREDICTOR v2.6<br>
</div>## Output produced at 2012-10-15 12:33:21<br>
<div>## 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>
</div>## CELL_TYPE : List of cell types and classifications for regulatory feature<br>
<div>## DISTANCE : Shortest distance from variant to transcript<br>
## PolyPhen : PolyPhen prediction<br>
## SIFT : SIFT prediction<br>
## Condel : Consensus deleteriousness score for an amino acid<br>
substitution based on SIFT and PolyPhen-2<br>
#Uploaded_variation Location Allele Gene Feature<br>
Feature_type Consequence cDNA_position CDS_position<br>
Protein_position Amino_acids Codons Existing_variation<br>
Extra<br>
1_94586536_C/A 1:94586536 A ENSG00000198691<br>
ENST00000370225 Transcript missense_variant,splice_region_variant<br>
153 66 22 K/N aaG/aaT -<br>
</div>PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.629);SIFT=tolerated(0.09)<br>
<div>1_94586536_C/A 1:94586536 A ENSG00000198691<br>
ENST00000535735 Transcript missense_variant,splice_region_variant<br>
146 66 22 K/N aaG/aaT -<br>
</div>PolyPhen=benign(0.235);Condel=neutral(0.343);SIFT=tolerated(0.07)<br>
<div>1_94586536_C/G 1:94586536 G ENSG00000198691<br>
ENST00000370225 Transcript missense_variant,splice_region_variant<br>
153 66 22 K/N aaG/aaC -<br>
</div>PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.629);SIFT=tolerated(0.09)<br>
<div>1_94586536_C/G 1:94586536 G ENSG00000198691<br>
ENST00000535735 Transcript missense_variant,splice_region_variant<br>
146 66 22 K/N aaG/aaC -<br>
</div>PolyPhen=benign(0.235);Condel=neutral(0.343);SIFT=tolerated(0.07)<br>
<br>
Cheers<br>
<span><font color="#888888"><br>
Will<br>
</font></span><div><div><br>
On 16 October 2012 07:36, binit treesa <<a href="mailto:binit.treesa@gmail.com" target="_blank">binit.treesa@gmail.com</a>> wrote:<br>
> Thank you for your help.<br>
><br>
> I verified all those things that you suggested. I feel there is no problem<br>
> with config and <a href="http://condel.pm" target="_blank">condel.pm</a>.<br>
><br>
> It would be much thankful, if you send me the output file that you<br>
> generated.<br>
><br>
><br>
> On Mon, Oct 15, 2012 at 5:10 PM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:<br>
>><br>
>> Hello again,<br>
>><br>
>> I still don't see these errors - perhaps your Condel configuration<br>
>> file is missing some values?<br>
>><br>
>> Also try updating your Condel.pm and config from the GitHub repository<br>
>> again.<br>
>><br>
>> Mine looks like:<br>
>><br>
>> > cat ~/.vep/Plugins/config/Condel/config/condel_SP.conf<br>
>> condel.dir='~/.vep/Plugins/config/Condel/'<br>
>><br>
>><br>
>> #------------------------------------------------------------------------------<br>
>> cutoff.HumVar.sift='0.15'<br>
>> cutoff.HumVar.polyphen='0.28'<br>
>> cutoff.HUmVar.condel='0.46'<br>
>><br>
>> #------------------------------------------------------------------------------<br>
>> max.HumVar.sift='1'<br>
>> max.HumVar.polyphen='1'<br>
>><br>
>> On 15 October 2012 11:42, binit treesa <<a href="mailto:binit.treesa@gmail.com" target="_blank">binit.treesa@gmail.com</a>> wrote:<br>
>> > Will McLaren,<br>
>> ><br>
>> > Thanks for spending time on this data.<br>
>> ><br>
>> > I rechecked the input data. There are no empty lines.<br>
>> > And I tried the format option in the VEP command as the input is in vcf<br>
>> > format.<br>
>> ><br>
>> > Command:<br>
>> ><br>
>> > perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i testinput3.vcf -format vcf -o<br>
>> > outputCondel.txt -sift b -polyphen b -plugin<br>
>> > Condel,/users/tbinit/.vep/Plugins/config/Condel/config,b,2<br>
>> ><br>
>> > But still I am getting the same output and showing only 50% completeness<br>
>> > in<br>
>> > calculating the consequences.<br>
>> ><br>
>> > Here attached the screen shot of VEP run and the output file generated.<br>
>> > Condel scores are pretty same as previous output.<br>
>> ><br>
>> > Can you please check this output (condel score) with the one that your<br>
>> > VEP<br>
>> > run generated with the the same input.<br>
>> ><br>
>> > Thanks<br>
>> > Treesa Binit<br>
>> ><br>
>> ><br>
>> >><br>
>> >><br>
>> >> ---------- 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<br>
>> >> a<br>
>> >> variant file. It executed succesfully and generated the output file .<br>
>> >> But when I executed this with the options for "sift, polyphen and<br>
>> >> condel<br>
>> >> plugin", it throws some erros. Eventhough it calculated all the score<br>
>> >> and<br>
>> >> 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<br>
>> >> here.<br>
>> >><br>
>> >> Details of the <a href="http://vep.pl" target="_blank">vep.pl</a> run is given below<br>
>> >><br>
>> >> Input File :test.txt<br>
>> >><br>
>> >> #CHROM_ID START ID REF ALT<br>
>> >> 1 94586536 . C A<br>
>> >> 1 94586536 . C G<br>
>> >><br>
>> >><br>
>> >> Output file : testOutput.txt<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<br>
>> >> substitution based on SIFT and PolyPhen-2<br>
>> >> #Uploaded_variation Location Allele Gene Feature<br>
>> >> Feature_type Consequence cDNA_position CDS_position<br>
>> >> Protein_position Amino_acids Codons Existing_variation<br>
>> >> Extra<br>
>> >> 1_94586536_C/A 1:94586536 A ENSG00000198691 ENST00000370225<br>
>> >> Transcript missense_variant,splice_region_variant 153 66 22<br>
>> >> K/N aaG/aaT -<br>
>> >><br>
>> >> PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.885);SIFT=tolerated(0.09)<br>
>> >> 1_94586536_C/A 1:94586536 A ENSG00000198691 ENST00000535735<br>
>> >> Transcript missense_variant,splice_region_variant 146 66 22<br>
>> >> K/N aaG/aaT -<br>
>> >> PolyPhen=benign(0.235);Condel=deleterious(0.583);SIFT=tolerated(0.07)<br>
>> >> 1_94586536_C/G 1:94586536 G ENSG00000198691 ENST00000370225<br>
>> >> Transcript missense_variant,splice_region_variant 153 66 22<br>
>> >> K/N aaG/aaC -<br>
>> >><br>
>> >> PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.885);SIFT=tolerated(0.09)<br>
>> >> 1_94586536_C/G 1:94586536 G ENSG00000198691 ENST00000535735<br>
>> >> Transcript missense_variant,splice_region_variant 146 66 22<br>
>> >> K/N aaG/aaC -<br>
>> >> PolyPhen=benign(0.235);Condel=deleterious(0.583);SIFT=tolerated(0.07)<br>
>> >><br>
>> >><br>
>> >> Command used<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<br>
>> >> -polyphen b -plugin<br>
>> >> Condel,/users/tbinit/.vep/Plugins/config/Condel/config,b --force<br>
>> >><br>
>> >> The status of the processing is shown<br>
>> >><br>
>> >> readline() on closed filehandle SIFT at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 136.<br>
>> >> readline() on closed filehandle POLYPHEN at<br>
>> >> /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<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 316, <GEN0> line 4.<br>
>> >> Use of uninitialized value $ref in length at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 349, <GEN0> line 4.<br>
>> >> Use of uninitialized value $alt in pattern match (m//) at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 352, <GEN0> line 4.<br>
>> >> Use of uninitialized value $alt in split at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 425, <GEN0> line 4.<br>
>> >> Use of uninitialized value $alt in pattern match (m//) at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 434, <GEN0> line 4.<br>
>> >> Use of uninitialized value $ref in concatenation (.) or string at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 501, <GEN0> line 4.<br>
>> >> Use of uninitialized value $alt in concatenation (.) or string at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 501, <GEN0> line 4.<br>
>> >> Use of uninitialized value $data[2] in string eq at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 501, <GEN0> line 4.<br>
>> >> Use of uninitialized value in pattern match (m//) at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 1944, <GEN0> line 4.<br>
>> >> Use of uninitialized value in substitution (s///) at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 1944, <GEN0> line 4.<br>
>> >> Use of uninitialized value in string eq at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 1945, <GEN0> line 4.<br>
>> >> Use of uninitialized value in pattern match (m//) at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> line 1950, <GEN0> line 4.<br>
>> >> Use of uninitialized value in concatenation (.) or string at<br>
>> >><br>
>> >> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm<br>
>> >> 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<br>
>> >> database<br>
>> >><br>
>> >><br>
>> >> [================================================================================================================================]<br>
>> >> [ 100% ]<br>
>> >> 2012-10-10 05:50:06 - Retrieved 9 transcripts (0 mem, 0 cached, 9 DB, 0<br>
>> >> duplicates)<br>
>> >> 2012-10-10 05:50:06 - Analyzing chromosome 1<br>
>> >> 2012-10-10 05:50:06 - Analyzing variants<br>
>> >><br>
>> >><br>
>> >> [================================================================================================================================]<br>
>> >> [ 100% ]<br>
>> >> 2012-10-10 05:50:08 - Calculating consequences<br>
>> >> [><br>
>> >> ] [ 0% ]Use of uninitialized value in subtraction (-) at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0><br>
>> >> line 4.<br>
>> >> Use of uninitialized value in subtraction (-) at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 212, <GEN0><br>
>> >> line 4.<br>
>> >> Use of uninitialized value in subtraction (-) at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0><br>
>> >> line 4.<br>
>> >> Use of uninitialized value in subtraction (-) at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 216, <GEN0><br>
>> >> line 4.<br>
>> >> [==============================================================><br>
>> >> ] [ 50% ]Use of uninitialized value in subtraction (-) at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0><br>
>> >> line 4.<br>
>> >> Use of uninitialized value in subtraction (-) at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 212, <GEN0><br>
>> >> line 4.<br>
>> >> Use of uninitialized value in subtraction (-) at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0><br>
>> >> line 4.<br>
>> >> Use of uninitialized value in subtraction (-) at<br>
>> >> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 216, <GEN0><br>
>> >> line 4.<br>
>> >><br>
>> >><br>
>> >> [================================================================================================================================]<br>
>> >> [ 100% ]<br>
>> >> 2012-10-10 05:50:11 - Processed 2 total variants (0 vars/sec, 0<br>
>> >> vars/sec<br>
>> >> total)<br>
>> >> 2012-10-10 05:50:11 - Finished!<br>
>> >><br>
>> >><br>
>> >> Thanks<br>
>> >> Treesa Binit<br>
>> >><br>
>> ><br>
>> ><br>
><br>
><br>
</div></div></blockquote></div><br>