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GA analysis: ModelSelectorBranchLocal.bf inputs (Read 1565 times)

Sarah

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GA analysis: ModelSelectorBranchLocal.bf inputs
Dec 5^th, 2006 at 3:21pm

I'm having trouble with the inputs expected by ModelSelectorBranchLocal.bf (the download of 11/21). First I'm prompted to choose a genetic code. I type "1" and then receive "Please choose an option." I type "1" again (or sometimes just hit enter) and then am asked to choose a codon file to analyze. I enter the file and am then prompted again to choose a codon file. If I enter the same file I then receive "This doesn't seem to be a valid Newick string file..." I've played around and sometimes entered the tree at this step, and then hit return when prompted for the tree. Then I'm asked to choose an evolutionary model two times and then the program appears to start running. If I don't enter the tree in advance, I tend to get an error message.

I'd love to write a script for these inputs once I understand what's expected.

I've had the same problem executing these commands via a terminal window from both a Mac and a Windows machine.

Sarah

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Sergei

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Datamonkeys are forever...

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Re: GA analysis: ModelSelectorBranchLocal.bf input
Reply #1 - Dec 5^th, 2006 at 3:36pm

Dear Sarah,

Not sure where this is coming from. The file REQUIRES an MPI environment to run though, so this could be the issue. Make sure you download a more recent version of the GA branch files, since the original one was missing some necessary files. Here's an example session on my cluster:

Code:

[sergei@monkey_supreme HYPHY_Source]$ mpirun -np 16 ./HYPHYMPI BASEPATH=/home/sergei/Latest/HYPHY_Source/ GABranch_2006/ModelSelectorBranchLocal.bf  

                        +-------------------+
                        |Choose Genetic Code|
                        +-------------------+


        (1):[Universal] Universal code. (Genebank transl_table=1).
        (2):[Vertebrate mtDNA] Vertebrate mitochondrial DNA code. (Genebank transl_table=2).
        (3):[Yeast mtDNA] Yeast mitochondrial DNA code. (Genebank transl_table=3).
        (4):[Mold/Protozoan mtDNA] Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Spiroplasma code. (Genebank transl_table=4).
        (5):[Invertebrate mtDNA] Invertebrate mitochondrial DNA code. (Genebank transl_table=5).
        (6):[Ciliate Nuclear] Ciliate, Dasycladacean and Hexamita Nuclear code. (Genebank transl_table=6).
        (7):[Echinoderm mtDNA] Echinoderm mitochondrial DNA code. (Genebank transl_table=9).
        (8):[Euplotid Nuclear] Euplotid Nuclear code. (Genebank transl_table=10).
        (9):[Alt. Yeast Nuclear] Alternative Yeast Nuclear code. (Genebank transl_table=12).
        (10):[Ascidian mtDNA] Ascidian mitochondrial DNA code. (Genebank transl_table=13).
        (11):[Flatworm mtDNA] Flatworm mitochondrial DNA code. (Genebank transl_table=14).
        (12):[Blepharisma Nuclear] Blepharisma Nuclear code. (Genebank transl_table=15).

 Please choose an option (or press q to cancel selection):1

(/home/sergei/Latest/HYPHY_Source/GABranch_2006/) Codon file to analyze:../data/hiv.seq


A tree was found in the data file:
(((((((((719:0.026535,136:0.011248):0.010815,135:0.057672):0.005853,(105r:0.007414,529:0.011129):0.000000):0.045023,317:0.016953):0.063552,6767:0.007903):0.061474,6760:0.002921):0.058089,9939:0.008796):0.084352,(159:0.007414,256:0.013253):-0.041823):-0.002767,113:0.023984,822:0.017431)

Would you like to use it:(Y/N)?y



Nucleotide a 6-character model string specification (e.g. HKY85 = 010010):?010010
[Preliminary Step 1] A total of 23 branches. Fitting a nucleotide model to approximate branch lengths...
[Preliminary Step 2] Nucleotide LogL = -1155.8
...

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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