config file error?

[Liang Wang]

Hi everyone:

     I just used bppml to estimate the parameters for my data. But I just got two output files (ML_dnd file) without any error info when using cmd "bppml param=ml.bpp". $(DATA).infos and $(DATA).params.txt have not been generated. Besides, the bppml run just a few seconds before it completed. I confused by the speed, as my data contains 2000+ sequences. I think there should be some error in my config file which I can not realized. I attached my data and config file. Is there anyone can tell me the error in my input data or config file?

     In addition, I used Coala model in this analysis. Just like I wrote in config file "model=Coala(exch=LG08,nbrAxes=1)". Is there any method to make me use an empirical model other than LG08 in this situation? If possible how can I wrote the model parameter?

     As the object of my research was to reconstruct the ancestral sequences, the input tree file should be rooted?

[Julien Y. Dutheil]

Hi Liang,

The behaviour is due to the option 'output.tree_ids.file': when set, bppml only outputs a tree with all ids. If you comment this option, the program will proceed with optimization. Note that bppml will most likely fail with so many sequences because of numerical underflow (unless you are using the development version of Bio++). Concerning the Coala model, it should be possible to use it in combination with an empirical model specified in the PAML syntax, such as:

model=Coala(exch=Empirical(name=mymodel, file=mymodel.dat),nbrAxes=1)

Hope this helps,

Julien.

[Liang Wang]

Hi Julien:
   Thank you for your patience. I just commet the output.tree_ids.file, and also modified the model like this "model=Coala(exch=Empirical(name=mymodel, file=Flu_All_it2.txt_PAML.txt),nbrAxes=1)". But aditional error was occured to me "ParameterNotFoundException: ParameterList::getSharedParameter('name').(root.MVA.MVA.RootAxPos0)". I guess this was the problem with parameter "nonhomogeneous.root_freq", which I set to "MVAprotein". But I can not figure out why this happened? When I change to use another model like LG08, this error was still occured to me. Please Please guide me how to fix this error! I also upload the screen output for your further evalution.

******************************************************************
*       Bio++ Maximum Likelihood Computation, version 2.3.1      *
*                                                                *
* Authors: J. Dutheil                       Last Modif. 06/06/17 *
*          B. Boussau                                            *
*          L. Gu茅guen                                            *
*          M. Groussin                                           *
******************************************************************

Parsing options:
Parsing file optionsFileBppML for options.
Alphabet type .........................: Proteic
Sequence file .........................: muscle.fa
Sequence format .......................: FASTA file
Sites to use...........................: all
Remove sites with gaps.................:
[======================================] 100%Done.
Number of sequences....................: 2004
Number of sites........................: 539
Input tree.............................: user
Input tree file .......................: rootedTree.nwk
Input tree format .....................: Newick
Number of leaves.......................: 2004
Output tree file ......................: H7_ML.dnd
Output tree format ....................: Newick
Branch lengths.........................: Input
Heterogeneous model....................: one_per_branch
Substitution model.....................: Empirical
Substitution model.....................: Coala
External frequencies initialization for: None
Parameter found........................: Coala.AxPos0=0
External frequencies initialization for: None
Parameter found........................: Coala.AxPos0=0
Distribution...........................: Gamma
Number of classes......................: 4
Parameter found........................: Gamma.alpha=1
- Category 0 (Pr = 0.25) rate..........: 0.136954
- Category 1 (Pr = 0.25) rate..........: 0.476752
- Category 2 (Pr = 0.25) rate..........: 1
- Category 3 (Pr = 0.25) rate..........: 2.38629
Rate distribution......................: Gamma
Number of classes......................: 4
Root frequencies ......................: MVAprotein
ParameterNotFoundException:
ParameterList::getSharedParameter('name').(root.MVA.MVA.RootAxPos0)