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

[Tom Madden]

Hi,
	I suspect that the problem reported below is one we fixed
in BLAST 2.0.9.  There was a missing thread join that seemed to
only cause problems on a DEC Alpha.  It does not seem to have
affected the results.  Please try this with the latest
binaries and write to toolbox@ncbi.nlm.nih.gov with details if
the problem still isn't fixed.

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: bmgustav@bioinfo.weizmann.ac.il
> Mime-Version: 1.0
> Date: Sat, 29 May 1999 18:45:11 +0300
> To: vsns-bcd-perl@lists.uni-bielefeld.de, toolbox@ncbi.nlm.nih.gov
> From: Gustavo Glusman <Gustavo@bioinformatics.weizmann.ac.il>
> Subject: Re: Bioperl: Bio::Tools::Blast->new on sequence file w/no hits,  
throws fatal exception. Any ideas?
> 
> At 11:22 -0700 28/5/99, Keith Allen wrote:
> >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.
> 
> We have also experienced this, actually at very high rates, and, as you
> mention, unpredictably.
> What I get on STDERR is:
> 
> Unhandled exception, code 0xe0ffe0000, in thread 3 at PC=0x3ff807b3868
> 
> The funny bit is that, error line or not error line, the blast gets executed.
> This happens (only) on a DEC Alpha. I can provide more details if needed.
> 
>      ____________________________________________________________
>      Gustavo Glusman              Founder/administrator of BioMOO
>      Gustavo@bioinfo.weizmann.ac.il    (public PGP key available)
>      http://bioinfo.weizmann.ac.il/Gustavo
>         Visit BioMOO, the biologists' virtual meeting place, at
>      ___________ http://bioinfo.weizmann.ac.il/BioMOO ___________
> 
> 

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