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

[Will McLaren]

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
>
>
>
> _______________________________________________
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> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
>
>
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