[ensembl-dev] Problem with BLAST setup

Youens-Clark, Ken kclark at cshl.edu
Mon May 6 23:18:20 BST 2013


I have set up a mirror of your BLAST databases using the v70 software.  Every request gives me the following error message:

-------------------- EXCEPTION --------------------
MSG: seq_region_name argument is required
STACK Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_region /usr/local/ensembl-grmblast/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm:201
STACK Bio::Search::HSP::EnsemblHSP::_map /usr/local/ensembl-grmblast/eg-plugins/common/modules/Bio/Search/HSP/EnsemblHSP.pm:436
STACK Bio::Search::Result::EnsemblResult::map_to_genome /usr/local/ensembl-grmblast/modules/Bio/Search/Result/EnsemblResult.pm:271
STACK Bio::Tools::Run::Search::parse /usr/local/ensembl-grmblast/modules/Bio/Tools/Run/Search.pm:1061
STACK (eval) /usr/local/ensembl-grmblast/modules/Bio/Tools/Run/Search.pm:1000
STACK Bio::Tools::Run::Search::dispatch /usr/local/ensembl-grmblast/modules/Bio/Tools/Run/Search.pm:1000
STACK (eval) /usr/local/ensembl-grmblast/modules/Bio/Tools/Run/Search.pm:935
STACK Bio::Tools::Run::Search::run /usr/local/ensembl-grmblast/modules/Bio/Tools/Run/Search.pm:935
STACK (eval) /usr/local/ensembl-grmblast/perl/multi/blastview:281
STACK (eval) /usr/local/ensembl-grmblast/perl/multi/blastview:281
STACK (eval) (eval 770):1
STACK EnsEMBL::Web::Apache::SpeciesHandler::handler_species /usr/local/ensembl-grmblast/modules/EnsEMBL/Web/Apache/SpeciesHandler.pm:123
STACK EnsEMBL::Web::Apache::Handlers::handler /usr/local/ensembl-grmblast/modules/EnsEMBL/Web/Apache/Handlers.pm:369
STACK (eval) /usr/local/ensembl-grmblast/perl/multi/blastview:0
STACK toplevel /usr/local/ensembl-grmblast/perl/multi/blastview:0
Date (localtime)    = Mon May  6 18:10:56 2013
Ensembl API version = 70
---------------------------------------------------

I've traced the problem to the module "Bio::Search::HSP::EnsembHSP::_map" line 192:

	my ($prefix, $hit_name) = split /\:/, $hit->seq_id, 2;

The "seq_id" is consistent an integer value, so $hit_name never gets anything useful.  Then this is used to set:

	$dbseq_meta{name} = $hit_name;

Which is then used here:

	my $seq_name = $dbseq_meta{name};

And then here:

	my $Slice = $SlAdaptor->fetch_by_region ( $coord_system_name, $seq_name, $start, $end, $hit->strand );

So that there's no $seq_name and hence the error MSG above.

Can you advise how to fix?  Our BLAST is non-functional until this gets fixed!

	http://dev.gramene.org/multi/blastview
 
--
Ken Youens-Clark
kclark at cshl.edu
Ware Lab/CSHL/USDA-ARS







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