[Bioperl-l] help me with "blastall call crashed:-1"

[Remo Sanges]

On Mar 15, 2005, at 4:18 PM, sasalacolla@@libero..it wrote:

> Hi, please help me. I tried to use psort, but i only got this message:
>
> Fatal error:
> ------------- EXCEPTION  -------------
> MSG: blastall call crashed: -1 /usr/bin/blastall -p  blastp
> -d  /usr/local/psort//conf/analysis/sclblast/gramneg/sclblast
> -i  /tmp/IBcvdGTw4w  -e  1e-09  -o  /tmp/NaRiG0fdH8  -F  F
>
> STACK
> Bio::Tools::Run::StandAloneBlast::_runblast 
> /usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:732
> STACK
> Bio::Tools::Run::StandAloneBlast::_generic_local_blast 
> /usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:680STACK
> Bio::Tools::Run::StandAloneBlast::blastall 
> /usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:536
> STACK
> Bio::Tools::Run::SCLBlast::blast 
> /usr/local/share/perl/5.8.4/Bio/Tools/Run/SCLBlast.pm:134
> STACK
> Bio::Tools::PSort::Module::SCLBlast::run 
> /usr/local/share/perl/5.8.4/Bio/Tools/PSort/Module/SCLBlast.pm:72
> STACK
> Bio::Tools::PSort::Pathway::__ANON__ 
> /usr/local/share/perl/5.8.4/Bio/Tools/PSort/Pathway.pm:194
> STACK
> Bio::Tools::PSort::Pathway::traverse 
> /usr/local/share/perl/5.8.4/Bio/Tools/PSort/Pathway.pm:157
> STACK
> Bio::Tools::PSort::classify 
> /usr/local/share/perl/5.8.4/Bio/Tools/PSort.pm:160
> STACK (eval) /usr/local/bin/psort:318
> STACK toplevel /usr/local/bin/psort:318

Please when you ask for help, consider to send the code that
is failing, in other ways we don't have a good starting point
to help you and many people will trash your message...

BTW
I have never used PSort.pm but your problem come from a blast
call, so my two cents from StandAloneBlast.pm considerations:

in your error message It seems to me that you at least has a wrong
definition of the local database directory, see here:

> -d  /usr/local/psort//conf/analysis/sclblast/gramneg/sclblast

this probably means that:

1 your BLASTDATADIR is defined to be /usr/local/psort/
Even if this is the right location you should avoid the final '/'
But probably your database is in /conf/analysis/sclblast/gramneg
folder right?

2 you have passed the database with the full path into your
    params: /conf/analysis/sclblast/gramneg/sclblast
    when you needed to simply use 'sclblast'

This is a cut from the code of the module:

If local BLAST databases are not stored in the standard
/data directory, the variable BLASTDATADIR will need to be set 
explicitly

You need to enable Blast to find the directory containing the databases.
This can be done in (at least) two different ways:
   1. define an environmental variable BLASTDATADIR:
       export BLASTDATADIR=/conf/analysis/sclblast/gramneg   or
   2. include a definition of an environmental variable BLASTDATADIR in
       every script that will
      use StandAloneBlast.pm.
	
      BEGIN {$ENV{BLASTDATADIR} = ''/conf/analysis/sclblast/gramneg"; }


HTH

Remo