[Bioperl-l] Primer 3: MSG: Can't open RESULTS

[Jason Stajich]

What version of bioperl-run are you on - this looks to already be  
fixed in CVS.

-jason
On May 12, 2005, at 11:11 AM, Greg Wilson wrote:

> Ok, I think I figured this out. The following line (***)  needs to  
> be added to Bio/Tools/Run/Primer3.pm:
>
> 356 # make a temporary file and print the instructions to it.
> 357 my ($temphandle, $tempfile)=$self->io->tempfile;
> 358 print $temphandle join "\n", @{$self->{'primer3_input'}}, "=\n";
> 359 open (RESULTS, "$executable < $tempfile|") || $self->throw 
> ("Can't open RESULTS");
> *** close $temphandle ||  $self->throw("Can't close TEMPFILE");
>
> The temporary file never gets closed so the file descriptors just  
> pile up until the overall script ends. This will clean them up as  
> soon as we do not need them any more.
>
> Not sure who needs to do the actual patching of the module in CVS  
> though.
>
> Greg
>
>
> Gregory Drake Wilson wrote:
>
>> I am resurrecting a question posted last June (archived here
>> http://bioperl.org/pipermail/bioperl-l/2004-June/016255.html)  
>> regarding
>> bioperl's usage of Primer3 because the issue continues to plague  
>> me. All
>> of my implementations die reliably after a fixed number of  
>> attempts at
>> generating primers with this error:
>> ------------- EXCEPTION  -------------
>> MSG: Can't open RESULTS
>> STACK Bio::Tools::Run::Primer3::run
>> /usr/lib/perl5/vendor_perl/5.8.2/Bio/Tools/Run/Primer3.pm:360
>> STACK toplevel ./primer_maker.pl:128
>> --------------------------------------
>> The offending line (360) is:
>>   open (RESULTS, "$executable < $tempfile|") || $self->throw 
>> ("Can't open
>> RESULTS");
>> As the old thread suggests it is probably a numer of open files  
>> issue.
>>
>>> lsof -c pri +Lr
>>>
>> returns an ever increasing amount of entries like:
>>  primer_ma 28830 gdw1  425u   REG    3,6     1140     0  807353
>> /tmp/twdZa7turz (deleted)
>> primer_ba 28830 drakos7  426u   REG    3,6     1170     0  807354
>> /tmp/QDJv6Mb8iV (deleted)
>> Does anyone know a way to make sure those file descriptors are  
>> cleaned up
>> after each primer generation?
>> Greg
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>
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