Is it an incongruent in result?

[nvgiap]

Dear Dr. Julien Yann Dutheil

Thank you very much for your reply.
I looked for partition-labeled tree in the file "Partitions output to file..............: orf3-1.partitions_BIC_free.dnd", the only partitions tree I found.
Am I right? Also, I copy a part of option file, given below.

Thank you very much indeed!
Best regards
Giap Nguyen


+-------------------------------------------------------------------------------------------------------+
output.model.file =                                                                     
output.log.file =                                                                              
output.tree.file = $(DATA).ml_nh_$(METHOD).nhx
output.tree.format = NHX
output.partitions.file = $(DATA).partitions_$(METHOD).dnd
output.partitions.record = $(DATA).partitions_record_$(METHOD).txt
output.model.file = $(DATA).model_$(METHOD).bpp
output.intermediate.models = yes
output.log.file = $(DATA).model_$(METHOD).log.txt
output.parameters.file = $(DATA).ml_nh_$(METHOD).parameters.csv

.........

Model description output to file.......: orf3-1.model_BIC_free.bpp
Output parameter table to..............: orf3-1.ml_nh_BIC_free.parameters.csv
Output partitions record to............: orf3-1.partitions_record_BIC_free.txt
Wrote tree to file ....................: orf3-1.ml_nh_BIC_free.nhx
Partitions output to file..............: orf3-1.partitions_BIC_free.dnd
+------------------------------------------------------------------------------------------------------------+

[Julien Yann Dutheil]

Dear Nguyen,

Then it starts to look like a bug indeed, if the wrong output file is
writen in the partition file. I am on vacations, so cannot look at
that now, but will put it on the todo list for when I am back One way
to circumvent the issue temporarily is to rerun mapnh by telling it to
stop immediately after a minimum is found, instead of looking at the
next 10 models.

Best,

Julien.

> --
>
>
>



--
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 530

§ Max Planck Institute for Terrestrial Microbiology
Department of Organismic Interactions
Marburg -- GERMANY

§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE

[Giap Nguyen]

Dear Dr. Julien Yann Dutheil

Thank you very much for your help! I am so sorry to bother you at this moment.
Wish you have a nice vacation!

Thank you so much!
Best regards
Giap Nguyen

[Julien Yann Dutheil]

Dear Nguyen,

I cannot reproduce the error. It might be that the bug has already
been solved. Which version of testnh are you using ? If you want I can
give a look at your files, if you would send me an archive with all
what is needed to run partnh.

All the best,

Julien.

[Giap Nguyen]

Dear Dr. Julien Yann Dutheil

 

I use the following link to obtain the package http://biopp.univ-montp2.fr/articles/download/#linux. I just ignored a warning message regarding doxygen installation. I tried to download TestNH from Git (updated version) but it seem complicated.

 

Thank for your suggestion, I include an archive that contain all information about my run.

 

Thank you very much for your help!

 

Best regards

Giap Nguyen

[Julien Yann Dutheil]

Dear Nguyen,

May I ask for the command line used to run partnh as well?

All the best,

Julien.

[Giap Nguyen]

Dear Dr. Dutheil

This is the command I typed: 

./partnh param=PartNH.bpp >& partnh_free_BIC.out

I specified the follows in a param file other than type on command line:

    input.cluster_tree.file=Mantellid.cluster_join.dnd\

    partition.test=BIC\

    METHOD=join_BIC

And could you please tell me what does '>&' in command mean?

Thank you very much!

Best regards

Giap Nguyen

[Julien Yann Dutheil]

Dear Nguyen,

Then I think I do nor have the right PartNH.bpp file, as these options
are missing.
>& is a bash operator, that redirect standard output and warnings to the specified file, instead of displaying them in the terminal.

All the best,

J.

[Julien Yann Dutheil]

Oups, my mistake, was running MapNH.bpp instead :s Sorry about that...

J.

[Julien Yann Dutheil]

Hi Nguyen,

Finally solved that bug, which occurred only when the homogenous model
(1 partition) was favored. It fixed on the source repository, and the
correction will be included in the next release.

Many thanks for reporting this issue,

All the best,

Julien.

On Tue, Aug 21, 2012 at 8:51 PM, Julien Yann Dutheil