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

Chris Fields cjfields at uiuc.edu
Fri Aug 10 18:04:20 EDT 2007


On Aug 10, 2007, at 4:48 PM, Torsten Seemann wrote:

>> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Might be wise to go ahead and add it to bugzilla so we can track it,  
along with the workaround.

chris


More information about the Bioperl-l mailing list