[Bioperl-l] ATTN: Matthew Laird & Elia----blastall call crashed from StandAloneBlast
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
> 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
Might be wise to go ahead and add it to bugzilla so we can track it,
along with the workaround.
More information about the Bioperl-l