[Bioperl-l] Problem using StandAloneFasta about 80000 times...

[Palle Villesen (BiRC)]

Ok, thanks for the help,

I'll go through StandAloneFasta and see if I can get it to work properly...

Right now I'll probably hack and just do less than 1019 runs at a 
time...  (And I hoped I would be less of a pain to the ensembl team by 
asking this mailing list, but it seems like they are everywhere :) )

Have fun,
Palle, BiRC

Jason Stajich wrote:

>sounds like problems that people have had for StandAloneBlast in the past.
>I went through StandAloneBlast with as much of a fine tooth comb as I
>could bear and made sure filehandles and program handles were closed.
>You may have to do this in StandAloneFasta as I don't think it has had
>this type of attention. It should be submitted as a bug for someone to
>track down (desperately seeking volunteers to help with bug
>fixing/tracking down...)
>
>Alternatively If you don't want to do this - can you write your
>program to generate the whole input file list for FASTA and then just run
>this as a single input to FASTA at the end?
>
>-jason
>
>On Thu, 24 Jul 2003, Palle Villesen wrote:
>
>  
>
>>Hi,
>>
>>I've made small program for running FASTA chromosomal coordinates
>>against other chromosomal coordinates (basically a simple test for
>>repeated sequence (LTR))...
>>
>>Everything runs smoothly except I get a STACK error after 1019 runs.
>>
>>1016    485     X       19107183        19107980        YES
>>19102529        19102843        19111836        19112151        314
>>9307    0.78    5.4e-150
>>1017    484     X       20157010        20158151        NO
>>1018    483     X       20543945        20544912        NO
>>1019    482     X       20582210        20583516
>>------------- EXCEPTION  -------------
>>MSG:
>>STACK Bio::Tools::Run::Alignment::StandAloneFasta::run
>>/a/home/serine/palle/bioperl-run/Bio/Tools/Run/Alignment/StandAloneFasta.pm:336
>>
>>I looked in the code (StandAloneFasta.pm) and found that it opens a
>>FASTARUN handle on line 336, and I couldn't find a close FASTARUN
>>anywhere, but since I'm still a rookie in perl I'm just confused...
>>
>>If I wrap my small program, so it is executed thousands of times, it
>>works... It's only when running the StandAloneFasta module directly I
>>get the error...
>>
>>Any help will be appreciated,
>>Palle
>>BiRC.dk
>>
>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>    
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
>  
>

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   Palle Villesen, Ph.D. 
   BiRC, Build. 090, University of Aarhus
   DK - 8000 Aarhus C, Denmark

   Http://www.daimi.au.dk/~biopv - +45 61708600
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