[Bioperl-guts-l] [Bug 2193] New: "Undefined sub-sequence" exception parsing NCBI blastp report

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jan 25 01:57:08 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2193

           Summary: "Undefined sub-sequence" exception parsing NCBI blastp
                    report
           Product: Bioperl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: torsten at csse.monash.edu.au


I am getting Bio::SearchIO exceptions when parsing some reports.
The reports are generated with "blastall -p blastp -F F -e 0.1 -b 20".
The same error occurs for blastall versions 2.2.14 and 2.2.15.
I am running bioperl-live.
I have attached problematic report and script to reproduce it.
Here is the message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Undefined sub-sequence (281,13). Valid range = 281 - 503
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.5/Bio/Root/Root.pm:359
STACK: Bio::Search::HSP::HSPI::matches
/usr/lib/perl5/site_perl/5.8.5/Bio/Search/HSP/HSPI.pm:691
STACK: Bio::Search::SearchUtils::_adjust_contigs
/usr/lib/perl5/site_perl/5.8.5/Bio/Search/SearchUtils.pm:460
STACK: Bio::Search::SearchUtils::tile_hsps
/usr/lib/perl5/site_perl/5.8.5/Bio/Search/SearchUtils.pm:206
STACK: Bio::Search::Hit::GenericHit::start
/usr/lib/perl5/site_perl/5.8.5/Bio/Search/Hit/GenericHit.pm:935
STACK: ./bug.pl:8
-----------------------------------------------------------


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