[Bioperl-l] StandAloneBlast on pre-formatted GenBank nt database

Georg Otto georg.otto at tuebingen.mpg.de
Thu Apr 6 10:39:43 EDT 2006


Hi,

I apologize if this is a FAQ, but I couldn't find a solution using google.

I downloaded the pre-formatted nt blast database from GenBank which is
split in five smaller databases with file extensions like this: nt.0[0-4].* 
It also comes with an alias file nt.nal
blastall works well like this:

blastall -p blastn -d nt

But unfortunately my Perl script, which starts a blast search using

Bio::Tools::Run::StandAloneBlast

and the same parameters as the blastall command above gives a warning
and an exception:

[blastall] WARNING: Could not find index files for database /Library/WebServer/Documents/blast/db/Volumes/Seahorse_HD2/blastdb/nt
[blastall] WARNING: BI867164: Could not find index files for database /Library/WebServer/Documents/blast/db/Volumes/Seahorse_HD2/blastdb/nt

------------- EXCEPTION  -------------
MSG: blastall call crashed: 256 /usr/local/bin/blastall -p  blastn  -d  "/Library/WebServer/Documents/blast/db/Volumes/Seahorse_HD2/blastdb/nt"  -i  /tmp/Wb5ThHwjEu  -o  /tmp/zvWomE5U3U 

STACK Bio::Tools::Run::StandAloneBlast::_runblast /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:732
STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:680
STACK Bio::Tools::Run::StandAloneBlast::blastall /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:536
STACK toplevel /Users/rglab/Georg/bin/run_blast.pl:53

--------------------------------------

The perl script works well with other databases, that are not split,
so my guess is that the blast search as it is called from bioperl can
not deal with the split database while blastall can.

Does anybody have an idea how to solve this?

Best,

Georg 



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