[Bioperl-l] Re: "Too many files open" with bl2seq

[Jamie Hatfield (AGCoL)]

I was having problems with the "too many files open" error using the
bl2seq module also.  I think I found a suitable patch.  If you take the
$report object returned from the $factory->bl2seq command and call
$report->close() once you're done with it, you shouldn't get that error
anymore.  By the way, oddly enough, this is only necessary when
$report->sbjctName is defined.  I assume this is because this is the
only time that something was actually returned.

Of course, maybe I just don't have the latest files.  Either way, this
should fix the problem for anyone who still has it... Maybe?

----------------------------------------------------------------------
Jamie Hatfield                              Room 541H, Marley Building
Systems Programmer                          University of Arizona
Arizona Genomics Computational              Tucson, AZ  85721
  Laboratory (AGCoL)                        (520) 626-9598

> -----Original Message-----
> From: bioperl-l-bounces at bioperl.org 
> [mailto:bioperl-l-bounces at bioperl.org] On Behalf Of Steven Cannon
> Sent: Thursday, April 17, 2003 8:56 AM
> To: Peter Schattner
> Cc: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Re: "Too many files open" with bl2seq
> 
> 
> Peter:
> 
> Thanks. Actually, eval didn't help, at least as I applied it -- the 
> program keeps chugging (and ignores the errors), but the blasts still 
> don't give output after the ~250th hit. So I still wonder if  
> the bl2seq 
> problem might be the origin of the bioperl bl2seq errors.
> 
> Steve
> 
> On Thursday, April 17, 2003, at 10:12 AM, Peter Schattner wrote:
> 
> > Steven Cannon wrote:
> >
> >> To second your '"Too many files open" with bl2seq' 
> question, I noticed
> >> something similar last month when trying to use bl2seq via 
> bioperl. So,
> >> apologies for re-posting, but maybe the extra details will 
> help someone
> >> spot the glitch. I see a different set of errors (MSG:  No 
> hit object
> >> found for bl2seq report  ... etc.) , but perhaps the 
> underlying cause 
> >> is
> >> the same.
> >>
> >
> > Steve
> >
> > Actually, these are two completely separate issues.  The 
> "MSG:  No hit 
> > object
> > found for bl2seq report" crash is a bug in BPbl2seq.pm (I think).  
> > Could you
> > submit this as a bug report?  I've seen this problem too and as a 
> > workaround
> > you can just surround the StandAloneBlast call to bl2seq in 
> an "eval", 
> > ignore
> > the error and (at least for me) everything works fine.
> >
> > The "Too many files open"  crash is something quite 
> different.  It has
> > nothing to do with Bioperl since it happens when running 
> bl2seq from the
> > command line as well.
> >
> > Peter
> >
> >
> 
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