I have downloaded variant effect predictor and EnsEMBL API for that my problems are,<br><br>1) After every reboot of system i have to give the PERL5LIB path, Why?<br>2) Variant effect predictor is taking too long to process given vcf file (~2000 line of SNP/INDELs)<br>
3) In the end it gives error, <br><br>[orf@localhost variant_effect_predictor]$ perl <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -i ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr1_q20_sort.vcf -o chr1.txt -s cow<br>
WARNING: Start 5959615 or end . coordinate invalid on line 92                                           <span style="color: rgb(255, 0, 0);">/ INDEL</span><br>WARNING: Start 30571012 or end . coordinate invalid on line 572                                        <span style="color: rgb(255, 0, 0);">/ INDEL</span><br>
WARNING: Start 64306203 or end . coordinate invalid on line 819                                        <span style="color: rgb(255, 0, 0);">/ INDEL</span><br>WARNING: Start 76575493 or end . coordinate invalid on line 895<span style="color: rgb(255, 0, 0);">                                        / INDEL</span><br>
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.<br><br>-------------------- EXCEPTION --------------------<br>
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, <a href="http://s.name">s.name</a>, s.somatic, vf.validation_status, vf.consequence_type, vf.class_so_id<br>
FROM ( (variation_feature vf, source s) <br>  LEFT JOIN failed_variation fv ON fv.variation_id = vf.variation_id ) <br> WHERE s.somatic = 0 AND <br>    (<br>        fv.variation_id IS NULL OR<br>        fv.subsnp_id IS NOT NULL<br>
    )<br>     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<br>       vf.source_id = s.source_id <br>': 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.<br>
<br>STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:522<br>STACK Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_fetch /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:495<br>
STACK Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_constraint /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:316<br>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<br>
STACK Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice /home/orf/EnsEMBL/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:175<br>STACK main::print_consequences <a href="http://variant_effect_predictor.pl:318">variant_effect_predictor.pl:318</a><br>
STACK toplevel <a href="http://variant_effect_predictor.pl:289">variant_effect_predictor.pl:289</a><br>Ensembl API version = 61<br>---------------------------------------------------<br><br clear="all"><br>-- <br>Ketan Padiya<div>
Research Fellow<br>Anand Veterinary College<br>Gujarat<br>India.<br>+91 9428969448</div><div style="display: inline;"></div><br>
<br><div id="WISESTAMP_SIG_6967"></div>