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BioPP / testnh

Suite of programs for the analysis of non-homogeneous substitution processes
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Missing process in construction of SubstitutionProcessCollection. #8

Open jdaron opened 1 month ago

jdaron commented 1 month ago

Dear mapnh developers,

I have been trying to reproduce the example provided in this tutorial (https://github.com/BioPP/supp-mat/tree/master/mapdNdS), but I am getting this error message I can not figure it out.

Do you have any idea how to solve it?

Many thanks Josquin

mapnh SEQ=simul_seq.fa MODEL=model_ml TREE=tree_ml param=map_per_branch.bpp

Parsing options: Parsing file map_per_branch.bpp for options. Variable 'PREF' is undefined and was ignored. Alphabet type .........................: Codon(letter=DNA) Genetic Code...........................: Standard Sequence file .........................: ./simul_seq.fa Sequence format .......................: FASTA file

Data 1 Sites to use...........................: all Remove sites with gaps.................: [======================================] 100%Done. Remove Stop Codons.....................: yes Number of sites........................: 2000 Branch lengths.........................: Input

Rate 1 WARNING!!! Parameter rate_distribution not specified. Default used instead: Constant() Distribution...........................: Constant Number of classes......................: 1

lgueguen commented 1 month ago

Hi,

indeed these example were for the older version of bio++. I have updated them.

Cheers, Laurent

EricDeveaud commented 4 weeks ago

hummmm

fresh build of testnh whith the following components.

build [rpm]:bpplib/bpplib-3 > for p in * ; do echo -n "$p: "; git -C $p rev-parse --short HEAD; done
bpp-core: 1bfa4a4
bpp-phyl: 7e01e377
bpp-popgen: 72de565
bpp-seq: 8850370

testnh fresh clone.

build [rpm]:testnh/testnh > git rev-parse --short HEAD
62bbcbd

using supp-mat fresh clone 

build [rpm]:testnh/testnh > cd ~/supp-mat/mapdNdS
build [rpm]:supp-mat/mapdNdS > git rev-parse --short HEAD
6a0d6da

gives me the following error

build [rpm]:supp-mat/mapdNdS > !ma
mapnh SEQ=simul_seq.fa MODEL=model_ml TREE=tree_ml param=map_per_branch.bpp
******************************************************************
*                     Map NH, version 2                          *
* Authors: J. Dutheil                       Created on  09/12/10 *
*          B. Boussau                       Modif. 17/12/11      *
*          L. Guéguen                       Last Modif. 28/11/17 *
******************************************************************

Parsing options:
Parsing file map_per_branch.bpp for options.
Variable 'PREF' is undefined and was ignored.
AttributesTools::parseOptions(). Parameter file not found.: model_ml.params
    from  bpp::BppApplication::BppApplication
    from  mapnh() [0x42c8ac]

???

Eric

lgueguen commented 3 weeks ago

Hi Eric,

you should not run mapnh first, but there are several other commands to be run before. Everything is explained in manip.pdf: the command bppml should build a model_ml.params, which will be read by mapnh.

Cheers, Laurent

btw: I just updated manip.pdf, because of a } error.

EricDeveaud commented 3 weeks ago

OK thahks for the explanations.

Eric

jdaron commented 1 week ago

Dear Laurent,

Thanks for your quick answer. I have been try again to run the example above, from the git hub repository, however I am getting the error message bellow.

The model I am getting in the file "model_ml.params" is:

Log likelihood = -868.78177553527712007053

Number of sites = 100

Substitution model parameters:

model=CodonRate(model=JC69())

Rate distribution parameters:

rate_distribution=Constant()

Also I am using version bppsuite version 2.4.0 since I am struggling to install the latest version of bpp and it may explain the issue I am facing.

Thanks in advance for your feedback. Josquin

Parsing options: Parsing file map_per_branch.bpp for options. Variable 'PREF' is undefined and was ignored. Parsing file model_ml.params for options. Variable 'PREF' is undefined and was ignored. Alphabet type .........................: Codon(letter=DNA) Genetic Code...........................: Standard Sequence file .........................: simul_seq.fa Sequence format .......................: FASTA file

Data 1 Sites to use...........................: all Remove Stop Codons.....................: no Number of sites........................: 100

Tree 1 WARNING!!! Warning, input.tree1 format set to Newick Number of trees in file................: 1 Number of leaves.......................: 6 Branch lengths.........................: Input

Rate 1 Distribution...........................: Constant Number of classes......................: 1

Model 32218016 Model '' unknown, or does not fit Codon(letter=DNA) alphabet. from bpp::BppOTransitionModelFormat::readTransitionModel from bpp::BppOBranchModelFormat::readBranchModel from bpp::PhylogeneticsApplicationTools::getBranchModels from bpp::BppPhylogeneticsApplication::getCollection from mapnh() [0x42cbc9]

lgueguen commented 14 hours ago

Hi, following mapdNdS tuto, in model_ml.params, you should not have CodonRate model, but YN98.

Could you give me you input/output for bppml?