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

[Palle Villesen]

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