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

[ketan padiya]

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?
2) Variant effect predictor is taking too long to process given vcf file
(~2000 line of SNP/INDELs)
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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