[Bioperl-l] Bio:Tools::Run::Alignment::ClustalW not cleaning up after itself

Ryan Golhar golharam at umdnj.edu
Fri May 11 20:20:41 UTC 2007

I'm running a large series of clustalw alignments.  After a large number of
alignments, my perl script would die indicating too many links were open.  I
checked my /tmp directory (while the script is running) and noticed that the
temp directory created for ClustalW are not removed until after the script
How can I force the cleanup of these directories after I am done with the

My code is essentially this;

$aln_factory = Bio::Tools::Run::Alignment::Clustalw->new();
$aa_aln = $aln_factory->align(\@aa_seqs);
open(STDOUT, ">&OLDOUT");
$dna_aln = &aa_to_dna_aln($aa_aln, \%dna_seqs);


More information about the Bioperl-l mailing list