BLAST jobs crashing - any ideas?

nospam at our.site nospam at our.site
Tue Mar 7 13:27:52 EST 2000


This message has been posted by:  Arne Mueller <a.mueller at REMOVE-THIS-TO-SENDicrf.icnet.uk>

Gary Williams wrote:
> 
> We are seeing increasing numbers of BLAST searches failing like this:
> 
> ---------------------------------------------------------------------------
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs",  Nucleic Acids Res. 25:3389-3402.
> 
> Query= Z92844, 151798 bases, CBD5EE91 checksum.
>          (151,798 letters)
> 
> Database: new
>            312,486 sequences; 300,934,448 total letters
> 
> Searching.......................................
> ---------------------------------------------------------------------------
> 
> With no further output or error messages.
> It exits with a status value of 1.

Hi All,

I had problems with blast version 2.0.6 (I guess), sometimes it crashed
and it took me while to look at the syslog of our server to find out
that it was killed by the operating system (IRIX 6.5). 

The reason was that blastpgp installed a signal handler to catch
segmentation faults and this handler itself caused a segmentation fault.
To prevent an endless recoursion it was killed by the os (that was the
message in the syslog). It's along time ago and I don't realy remember
;-( but I think blastpgp was terminated without printing any message.

Is there anything in your syslog?
 
	good luck,

	Arne

-- 
Arne Mueller
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX, U.K.
phone : +44-(0)171 2693405      | fax :+44-(0)171-269-3534
email : a.mueller at icrf.icnet.uk | http://www.bmm.icnet.uk





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