VectorSiteContainer::getSequencePosition()

[omotoso olatunde]

Good morning,

Please I have challenge parsing "option_file" to CoMap for co-substitution analysis.

Here is the std-out

***********************************************************

* This is CoMap        version 1.5.2       date: 11/03/15 *

*     A C++ shell program to detect co-evolving sites.    *

***********************************************************

Parsing options:

Parsing file option_file for options.

-*- Retrieve data and model -*-

Tree file..............................: /media/science/enhancer/workfile/myedit/comaptree/ENSG00000284701.txt.tree

Number of leaves.......................: 25

Number of sons at root.................: 2

Alphabet type .........................: DNA

Sequence file .........................: /media/science/enhancer/workfile/myedit/comapseq/ENSG00000284701_NT_filter.fasta

Sequence format .......................: FASTA file

Sites to use...........................: all

Remove sites with gaps.................:

[======================================] 100%Done.

Remove unresolved sites................:

[======================================] 100%Done.

Heterogeneous model....................: no

Substitution model.....................: GTR

External frequencies initialization for: None

Parameter found........................: GTR.a=1

Parameter found........................: GTR.b=1

Parameter found........................: GTR.c=1

Parameter found........................: GTR.d=1

Parameter found........................: GTR.e=1

Constraint match at parameter GTR.theta, badValue = 1.000000 ]1e-06; 0.999999[

Parameter found........................: GTR.theta=0.999999

Constraint match at parameter GTR.theta1, badValue = 1.000000 ]1e-06; 0.999999[

Parameter found........................: GTR.theta1=0.999999

Constraint match at parameter GTR.theta2, badValue = 1.000000 ]1e-06; 0.999999[

Parameter found........................: GTR.theta2=0.999999

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

SequenceNotFoundException: VectorSiteContainer::getSequencePosition().(Panthera_tigris)

first, I don't know what it means by "VectorSiteContainer" and don't know how to fix it.

Second, is my substitution model input correct? what I want is  GTR + gamma + I  to replicate the MBE (2005) paper on CoMap. All help is highly appreciated. 

Thank you very much

[Julien Y. Dutheil]

Hi,

This error message typically means that the sequence names in the imput tree do not match the ones in the sequence file. Here, it seems that the tree has a leaf named Panthera_tigris, which is not found in the alignment. Sometimes, this error is due to a wrong file format (like a windows file on a linux machine), which adds invisible cariage return characters at the the end of the sequence names.

I hope this helps,

Julien.

[omotoso olatunde]

Thank you @Professor Julien, you were right, some names were modified by the Time Tree that I forgot to change in the fasta file.
I just used a single file to test-run the  program, I plan to iterate it over some 10,000 files using "for loop". However, my current concern is the substitution model; how do I indicate as part of the model, the invariant regions (I)?  I plan to run the GTR + G + I, but can't figure out the I from the manual 

"""from the standout, this indicate the Gamma:

 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""""

looking forward to your feedback, I am very grateful.