[ensembl-dev] problem in variant effect predictor stand alone

ketan padiya ketanmicro at gmail.com
Wed Feb 16 04:08:04 GMT 2011


Thanks for reply, It worked well.

One more question for INDEL, variant_effect_predictor perl script don't
recognize INDEL string and gives warning like,

WARNING: Invalid allele string atggtccaatggtccaa/atggtccaa on line 92
WARNING: Invalid allele string aaaa/aaa on line 1249
WARNING: Invalid allele string cc/c on line 1378


On Tue, Feb 15, 2011 at 6:37 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Dear Ketyan,
>
> On 15 February 2011 20:13, ketan padiya <ketanmicro at gmail.com> wrote:
>
>> I have downloaded variant effect predictor and EnsEMBL API for that my
>> problems are,
>>
>> 1) After every reboot of system i have to give the PERL5LIB path, Why?
>>
>
> You can configure your system to load this PERL5LIB automatically every
> time it starts. How you do this depends on what type of system you are
> using. For example, if you are using the CSH shell system, you can edit the
> file named ".cshrc" in your home directory, then add lines like:
>
> setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl/modules
> setenv PERL5LIB ${PERL5LIB}:${HOME}/srcl/ensembl-compara/modules
> setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl-functgenomics/modules
> setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl-variation/modules
>
> Or, if you use Bash, you can add the lines to ".bashrc", also in your home
> directory:
>
> PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-live
> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules
> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules
> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-functgenomics/modules
> export PERL5LIB
>
>
>
>> 2) Variant effect predictor is taking too long to process given vcf file
>> (~2000 line of SNP/INDELs)
>>
>
> For this and point 3), I recommend you try adding the following flags to
> your command:
>
> perl variant_effect_predictor.pl -i
> ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr1_q20_sort.vcf -o chr1.txt
> -format vcf -s cow -w -b 5000
>
> Using -format forces the program to read your file as a VCF.
>
> Using -w means the script runs in "whole-genome" mode, which is better
> suited to large data sets that cover, for example, one chromosome. You
> should make sure when you use this that the VCF input file is sorted by
> chromosome and then position.
>
> Setting a larger buffer size with -b helps whole genome mode work faster.
>
> Please note that the -w option is only available from version 61 of
> Ensembl.
>
> Thanks and good luck!
>
> Will McLaren
> Ensembl Variation
>
>
>
>> 3) In the end it gives error,
>>
>> [orf at localhost variant_effect_predictor]$ perl
>> variant_effect_predictor.pl -i
>> ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr1_q20_sort.vcf -o chr1.txt
>> -s cow
>> WARNING: Start 5959615 or end . coordinate invalid on line
>> 92                                           / INDEL
>> WARNING: Start 30571012 or end . coordinate invalid on line 572
>>                              / INDEL
>> WARNING: Start 64306203 or end . coordinate invalid on line 819
>>                              / INDEL
>> WARNING: Start 76575493 or end . coordinate invalid on line 895
>>                              / INDEL
>> DBD::mysql::st execute failed: Lost connection to MySQL server during
>> query at
>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line
>> 521, <GEN0> line 1006.
>>
>> -------------------- EXCEPTION --------------------
>> MSG: Detected an error whilst executing SQL 'SELECT
>> vf.variation_feature_id, vf.seq_region_id, vf.seq_region_start,
>> vf.seq_region_end, vf.seq_region_strand, vf.variation_id, vf.allele_string,
>> vf.variation_name, vf.map_weight, s.name, s.somatic,
>> vf.validation_status, vf.consequence_type, vf.class_so_id
>> FROM ( (variation_feature vf, source s)
>>   LEFT JOIN failed_variation fv ON fv.variation_id = vf.variation_id )
>>  WHERE s.somatic = 0 AND
>>     (
>>         fv.variation_id IS NULL OR
>>         fv.subsnp_id IS NOT NULL
>>     )
>>      AND vf.seq_region_id = 142972 AND vf.seq_region_start <= 23402307 AND
>> vf.seq_region_end >= 23402307 AND vf.seq_region_start >= 23401807  AND
>>        vf.source_id = s.source_id
>> ': DBD::mysql::st execute failed: Lost connection to MySQL server during
>> query at
>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line
>> 521, <GEN0> line 1006.
>>
>> STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch
>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:522
>> STACK Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_fetch
>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:495
>> STACK
>> Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_constraint
>> /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:316
>> STACK
>> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_constraint
>> /home/orf/EnsEMBL/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:121
>> STACK
>> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice
>> /home/orf/EnsEMBL/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:175
>> STACK main::print_consequences variant_effect_predictor.pl:318
>> STACK toplevel variant_effect_predictor.pl:289
>> Ensembl API version = 61
>> ---------------------------------------------------
>>
>>
>> --
>> Ketan Padiya
>> Research Fellow
>> Anand Veterinary College
>> Gujarat
>> India.
>> +91 9428969448
>>
>>
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>>
>>
>


-- 
Ketan Padiya
Research Fellow
Anand Veterinary College
Gujarat
India.
+91 9428969448
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110216/4c3af1ee/attachment.html>


More information about the Dev mailing list