Deep recursion on subroutine

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Deep recursion on subroutine

Qunfeng
Hi,

I am using bioperl (5.8.0, linux) to work on a UPGMA tree (newick format,
generated by PHYLIP).  My code works well on a small tree. However, when I
applied it to a big (ugly) tree, it produces the following error msg. Has
anybody encountered a similar problem? Is this triggered by any invalid
part of my tree? Thanks!

Qunfeng
===========Error message begins =====================
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::Node::height" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
=========Error msg ends==============================================

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Re: Deep recursion on subroutine

Jason Stajich
Without an actual example tree it is hard to really help you very much.

A simple code example which can reproduce the problem and the  
offending tree should be submitted (please attach and don't just  
paste the datafile into the comment) as part of  the bug report.

http://bugzilla.open-bio.org/

You should also mention what version of Bioperl you are using.

-jason
On Nov 30, 2005, at 4:46 PM, Qunfeng wrote:

> Hi,
>
> I am using bioperl (5.8.0, linux) to work on a UPGMA tree (newick  
> format, generated by PHYLIP).  My code works well on a small tree.  
> However, when I applied it to a big (ugly) tree, it produces the  
> following error msg. Has anybody encountered a similar problem? Is  
> this triggered by any invalid part of my tree? Thanks!
>
> Qunfeng
> ===========Error message begins =====================
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>  
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>  
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>  
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>  
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>  
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine  
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> =========Error msg ends==============================================
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12


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Re: Deep recursion on subroutine

Jonathan Arthur
In reply to this post by Qunfeng
Hello Qunfeng,

I have not seen this specifically with bioperl, but have had it occur
once or twice in my own code and have always traced the problem back to
an error in the tree where one node is its own ancestor, thereby causing
an infinite recursion when you attempt to find all descendants from that
node.

If each node has a unique identifier, and if the tree is not too large,
you could find the offedning node with a small script to traverse the
tree, testing the unique identifer of each node against a list of all
the nodes seen before and dying when it sees offending node again.

Cheers,

Jonathan

Qunfeng wrote:

> Hi,
>
> I am using bioperl (5.8.0, linux) to work on a UPGMA tree (newick
> format, generated by PHYLIP).  My code works well on a small tree.
> However, when I applied it to a big (ugly) tree, it produces the
> following error msg. Has anybody encountered a similar problem? Is
> this triggered by any invalid part of my tree? Thanks!
>
> Qunfeng
> ===========Error message begins =====================
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents"
> at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> =========Error msg ends==============================================
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l



--
Dr Jonathan Arthur
Sesqui Lecturer in Bioinformatics
Central Clinical School, Faculty of Medicine and SUBIT
Medical Foundation Building, K25
University of Sydney
Ph: +61 2 9036 3132
Email: [hidden email]


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solved Re: Deep recursion on subroutine

Qunfeng
Hello Jason and Jonathan,

Thanks for your help. Jason figures out the problem "
This is just Perl complaining because the recursion is deep because there are
so many levels in your tree (449 deep).  It thinks it hit a snag because it
doesn't expect to usually have a recursive call go that many levels.

You can make the warnings go away by adding this
no warnings 'recursion';"

Qunfeng
At 04:39 PM 11/30/2005, Jonathan Arthur wrote:

>Hello Qunfeng,
>
>I have not seen this specifically with bioperl, but have had it occur once
>or twice in my own code and have always traced the problem back to an
>error in the tree where one node is its own ancestor, thereby causing an
>infinite recursion when you attempt to find all descendants from that node.
>
>If each node has a unique identifier, and if the tree is not too large,
>you could find the offedning node with a small script to traverse the
>tree, testing the unique identifer of each node against a list of all the
>nodes seen before and dying when it sees offending node again.
>
>Cheers,
>
>Jonathan
>
>Qunfeng wrote:
>
>>Hi,
>>
>>I am using bioperl (5.8.0, linux) to work on a UPGMA tree (newick format,
>>generated by PHYLIP).  My code works well on a small tree. However, when
>>I applied it to a big (ugly) tree, it produces the following error msg.
>>Has anybody encountered a similar problem? Is this triggered by any
>>invalid part of my tree? Thanks!
>>
>>Qunfeng
>>===========Error message begins =====================
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::Node::height" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>Deep recursion on subroutine "Bio::Root::Root::DESTROY" at
>>/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
>>=========Error msg ends==============================================
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>[hidden email]
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>--
>Dr Jonathan Arthur
>Sesqui Lecturer in Bioinformatics
>Central Clinical School, Faculty of Medicine and SUBIT
>Medical Foundation Building, K25
>University of Sydney
>Ph: +61 2 9036 3132
>Email: [hidden email]
>
>
>_______________________________________________
>Bioperl-l mailing list
>[hidden email]
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://portal.open-bio.org/mailman/listinfo/bioperl-l
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