[Bioperl-l] dn/ds code from PAML howto not working

[Amir Karger]

A client of mine stole the pairwise Ka/Ks code from the "Running PAML
from within Bioperl" section of the PAML HOWTO. It mostly seems to be
running fine. However, when we say
	$result = $parser->next_result;

we get an undef $result. 

1) Is there something I can look for in the output files to show me
whether it's a problem with Bioperl itself (Never!) or with CODEML?

2) Is there a previously known issue with Bioperl's incorrectly reading
such files? Bio::Root::Version says it's 1.5, by the way.

3) Something else I haven't thought of?

Thanks,

Amir Karger
Research Computing, Life Sciences Division
Harvard University