[Bioperl-guts-l] [Bug 2977] TreeIO problems

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Feb 4 03:53:45 EST 2010


http://bugzilla.open-bio.org/show_bug.cgi?id=2977


online at davemessina.com changed:

           What    |Removed                     |Added
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                 CC|                            |online at davemessina.com




------- Comment #5 from online at davemessina.com  2010-02-04 03:53 EST -------
Hi Sandra,

I'm having a little bit of trouble reproducing the problem you're seeing.

The sequence file you uploaded contains all of the sequences on one line,
they're not aligned, and they're not the right length to be codons (385 not
evenly divisible by 3). The script you uploaded does a lot of things besides
run codeml, so it's a bit tricky to figure out what's going on. The part which
hands the tree to PAML seems to be commented out (line 360).  Also, it requires
as input some files I don't have, such as "orthologous_teste.txt".

If I take the code out which reads in the treefile, though (lines 340-349), and
make a test script with that, I get warnings:
--------------------- WARNING ---------------------
MSG: cannot call add_tag_value with an undefined value (B)
---------------------------------------------------

And that is due to this line in your code:
                      -internal_node_id => 'bootstrap',

which asks that internal node ids in the tree be set to the bootstrap value,
but your tree does not contain any bootstrap values. 

If you remove that line, the warnings go away.

Now, I know you said you were able to run codeml successfully outside of
BioPerl, so there very well may still be a problem in the BioPerl code. To
diagnose that, what I would need from you is:
- the file of multiply aligned DNA sequences that you pass to codeml
- the codeml.ctl file you use
- the codeml output files that you get from a successful run

And, ideally, a small test script which would try to run codeml using BioPerl
with that exact same input data and settings, and the complete output from
running that script.

Dave


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