[Bioperl-l] Memory Leak in Bio::SearchIO

[Torsten Seemann]

> taking up and huge amount of RAM. For a single job of 10000 queries it
> can consume as much as a couple hundred Mb inside an hour. I realize

>  my $result = $connector->getQueryResult($query_id);
>                 my $searchio = new Bio::SearchIO(-format => "blast",
>                 while (my $o_blast = $searchio->next_result()) {
>                         my $clone_id = $o_blast->query_name();
>                         my $statement = $bdbi->form_push_SQL ($o_blast, $clone_id, 5); }

Some comments:

Have you considered that whatever class/module $bdbi belongs to is 
causing the problem? ie. is it keeping a reference to $o_blast around?

Are you aware that Perl garbage collection does not necessarily return 
freed memory back to the OS? This may affect how you were measuring 
"memory usage".

-- 
Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia