[Bioperl-l] Blast return codes

[Matthew Laird]

Thanks for the replay, the error is as follows:

Fatal error:
------------- EXCEPTION  -------------
MSG: blastall call crashed: -1 /usr/local/blast/blastall -p  blastp  -d  
/usr/local/psort/conf/analysis/sclblast/sclblast  -i  /tmp/rvtNYtglud  -e  
1e-09  -o  /tmp/jFVFD1Pxt3

STACK Bio::Tools::Run::StandAloneBlast::_runblast 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/StandAloneBlast.pm:633
STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/StandAloneBlast.pm:603
STACK Bio::Tools::Run::StandAloneBlast::blastall 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/StandAloneBlast.pm:489
STACK Bio::Tools::Run::SCLBlast::blast 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/SCLBlast.pm:83
STACK Bio::Tools::PSort::Module::SCLBlast::run 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/PSort/Module/SCLBlast.pm:34
STACK Bio::Tools::PSort::Pathway::__ANON__ 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/PSort/Pathway.pm:154
STACK Bio::Tools::PSort::Pathway::__ANON__ 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/PSort/Pathway.pm:156
STACK Bio::Tools::PSort::Pathway::traverse 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/PSort/Pathway.pm:117
STACK Bio::Tools::PSort::classify 
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/PSort.pm:120
STACK (eval) /usr/local/psort/bin/psort:186
STACK toplevel /usr/local/psort/bin/psort:186

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

I modified bioperl to make a copy of the input file just before it 
executes the command thinking it could be a problem with the sequence.  
Unfortuantely when I then run the command by hand with that exact same 
input file I receive an exit status of 0.

It's also even more odd that the exact same installation steps on the 
exact same flavour of linux with the exact same version of perl works on a 
different machine.  It seems to be about a 50-50 success rate when I try 
it on various machines.

This produce any thoughts on what might be going on with blast and 
bioperl?  Thanks.


On Tue, 9 Dec 2003, Joseph Bedell wrote:

> 
> Hi Matthew,
> 
> I didn't see that anyone answered this question for you. See my comments
> below.
> 
> >-----Original Message-----
> >From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
> >bounces at portal.open-bio.org] On Behalf Of Matthew Laird
> >Sent: Friday, December 05, 2003 2:27 PM
> >To: bioperl-l at bioperl.org
> >Subject: [Bioperl-l] Blast return codes
> >
> >This is on the fringe of being off-topic... but still relivant. :)
> >
> >I've been trying to google around to find documentation regarding
> return
> >codes Blast gives upon exit.  Is there a list of return codes and
> >conditions that cause non-zero return codes?
> 
> No, there is no such list. We recently wrote an O'Reilly book on BLAST
> but we did not track down the return codes. We'll probably do that for
> the next edition. ;)
> 
> >
> >The reason I ask is I'm having a problem calling Blast from bioperl.
> For
> >some reason Blastall is returning a -1 exit code which of course causes
> >bioperl to throw an exception.  However I have modified my local
> install
> >of bioperl to tell me the exact command that was being run.  I've then
> run
> >this exact command with the exact same input files from the command
> line
> >and a standard 0 exit code is returned.  Might anyone have any thoughts
> on
> >why Blastall would be returning a -1 exit code?
> 
> I believe that all the return codes from blastall are positive integers.
> A -1 return code may signify a problem with the system call from PERL.
> The error messages are usually pretty comprehensive. Can you send the
> error message that's produced?
> 
> Thanks,
> Joey
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Joseph A Bedell, Ph.D.
> Director, Bioinformatics
> Orion Genomics, LLC
> 4041 Forest Park Ave.
> St. Louis, MO 63108
> (314)615-6979; fax:(314)615-6975
> http://www.oriongenomics.com
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
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> 

-- 
Matthew Laird
SysAdmin/Web Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University