Bioperl: Bio::Tools::Blast->new on sequence file w/no hits, throws fatal exception. Any ideas?

[Tom Madden]

Hi,
	you seem to be addressing two issues in this email.  One might be
related to a problem we fixed on DEC Alpha's for version 2.0.9.  Please
try the latest binaries and write to toolbox@ncbi.nlm.nih.gov if you
still experience a segfault.  The other problem is a complaint about
BLAST returning an uninformative exit status.  We'll improve this.

regards,

Tom Madden, Ph.D.
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health
Bldg. 38A, Rm. 8N-805
8600 Rockville Pike
Bethesda, Maryland  20894  USA

301-435-5991
301-480-9241 FAX

madden@ncbi.nlm.nih.gov

> X-Sender: allen@mailhost.deltagen.com
> Mime-Version: 1.0
> Date: Fri, 28 May 1999 11:22:00 -0700
> To: vsns-bcd-perl@lists.uni-bielefeld.de
> From: Keith Allen <allen@deltagen.com>
> Subject: Re: Bioperl: Bio::Tools::Blast->new on sequence file w/no hits, 
throws fatal exception. Any ideas?
> Cc: toolbox@ncbi.nlm.nih.gov
> 
> 
> I'd like to add a related issue into this thread, and that is the
> overall problem of handling NCBI Blast2.0x errors.  We run a number
> of scripts where sequences are sequentially fed to blast, and then
> we do one thing or another with the output stream.  But we were
> finding that at some rate blast returns a segfault.  I tried to
> trap these events by saying "if $? == 11 print the query and the
> blast command string to a logfile", but when I looked at the results
> there wasn't anything wrong.  Nor does it fail at a predictable
> place in a file containing multiple sequences.  It just happens
> at random, and it will even happen at the command line when running
> a single sequence.
> 
> The solution we came up with is simply to resubmit the blast query
> if we get exit status 11 back, up to some reasonable $MAX_RESUBMIT.
> I have yet to see it require more than a single resubmit.
> But this is an incomplete solution to handling blast errors
> because the program takes such a liberal view of what sort of
> exit status it should hand back to you.
> 
> Consider the following script running NCBI blast 2.0.8 on Solaris 2.6.
> The real database is called targetdb, and there is a real file called
> "query".
> 
> #!/usr/bin/perl
> 
> $result = `blastall -pblastn -dtargetdb -iquery -e1E-2`;
> print "normal run:  $?\n";
> 
> $result = `blastall -pbalstn -dtargetdb -iquery -e1E-2`;
> print "balstn:  $?\n";
> 
> $result = `blastall -pblastn -dtastdb -iquery -e1E-2`;
> print "no db:  $?\n";
> 
> $result = `blastall -pblastn -dtargetdb -inoquery -e1E-2`;
> print "no query:  $?\n";
> 
> 
> This produces the following output on stdout:
> 
> ____________________________
> normal run:  0
> [blastall] FATAL ERROR: Only blastn, blastp, blastx, tblastn tblastx is 
allowed
> 
> balstn:  0
> [blastall] WARNING: Could not find index files for database tastdb
> [blastall] WARNING: Could not find index files for database tastdb
> [blastall] WARNING: Could not find index files for database tastdb
> no db:  0
> [blastall] FATAL ERROR: blast: Unable to open input file noquery
> 
> no query:  0
> _____________________________
> 
> 
> I see two fatal errors here, and a third that certainly ought to be considered
> fatal, since it prevents the program from running, but they all return
> an exit status of 0.  Not to be critical of the nice folks at NCBI, but
> this is not the behaviour I would have expected, and it means the exit
> status is of no value for making sure the job went as expected.  You
> either have to capture and parse STDERR, or parse the blast output (which
> is what we do) to make sure things went OK.
> 
> How is this stuff being handled in the current blast modules?  I haven't
> run through this stuff with WUBlast, is it handled any better?
> 
> 
> 					-Keith Allen
> 
> 
> 
> -----------------------------------------
> Keith Allen, PhD
> Bioinformatics Specialist
> Deltagen, Inc
> 1031 Bing St.
> San Carlos, CA 94070
> 650 610-6826
> 
> 

=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================