[Bioperl-l] ATTN: Matthew Laird & Elia----blastall call crashed from StandAloneBlast

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Fri Aug 10 17:48:56 EDT 2007


> Interestingly, I found the message in bioperl-l from Matthew Laird 2005 "Blastall & StandAloneBlast". "...the Odd thing is, Blast DOES run.  If one comments out this line in StandAloneBlast.pm, the execution succeeds perfectly fine". It seemed to be mysterious when I uncommented the " $self->throw("$executable call crashed: $? $! $commandstring\n") unless ($status==0) ;" line, the blastall runs. The only difference from what Matthew saw is that, when I did not uncomment the line, blastall DID NOT run.

Yes, Matthew is one of the authors of PSORTB and I spent a bit of time
last year trying to fix this problem (unsuccessfully). The PSORTB docs
http://www.psort.org/downloads/index.html
explain how to get around this problem just as Guojun describes. I use
a custom BioPerl installation just for PSORTB!

 I was under the impression it was already filed as a bug, but my
searching indicates this is not so.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University


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