[Bioperl-l] exonerate

alan alan at tll.org.sg
Sun Sep 30 21:53:07 EDT 2007


Hi,


>> I am calling exonerate.pm within my script while attempting to  
>> align cDNA  to multiple genomic fragments. After processing about  
>> 120+ genomic fragments my code crashes with the following error:
>>
>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>> aborting...
>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF / 
>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/ 
>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/ 
>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>
>> The code in Exonerate.pm closes the tmpfile at the end of the  
>> routine yet I get the error message about "too many open files".
>> Any suggestions on how I should be closing these files?
>>
>>
>> Extract from my code that runs exonerate is listed below.
>>
>> foreach my $f(@files) {
>>   next unless (-f  "$dir/$f");
>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>   my $query_obj = $q_in->next_seq();
>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", - 
>> format=>"Fasta");
>>   my $target_obj = $target_in->next_seq();
>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>
>>   [code for parsing the data.......]
>>
>>   $exonerate_io->close; #tried this line out of desperation but it  
>> did not help :-)
>> }
>>
>> thanks
>> alan
>>
>>
>>
>> Alan Christoffels
>> Computational Biology Group
>> Temasek LifeSciences Laboratory
>> 1 Research Link
>> National University of Singapore
>> Singapore
>> 117604
>> Tel: +65 68744945
>> Fax: +65 68727007
>> Lab webpage: http://www.tll.org.sg/alan.asp
>>
>>
>



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