running JukesCantorTRNK.Rev

[hscarter]

when I try to run revbayes with this file I get the following errors

source("JukesCantorTRNK.Rev") Processing file "JukesCantorTRNK.Rev" Error: You used a non-model object ( type=NULL ) to create a constant node. Only model objects can be used for constant nodes. Error: Problem processing line 20 in file "JukesCantorTRNK.Rev"

I don't know what it means by non-model object or what its using as one and I can't see the problem with line 20. I edited that line but I'm pretty sure it follows the same format as the original line you used in JukesCantor.Rev for the bayes_intro assignment. JukesCantorTRNK.txt

[caseywdunn]

I took a look at JukesCantorITS.Rev to isolate the problem. I executed the commands from the file interactively. Reading in the data matrix gives an error, though it is a bit cryptic:

> data <- readDiscreteCharacterData("ITScombined.aligned.nex")
Error:  You used a non-model object ( type=NULL ) to create a constant node. Only model objects

can be used for constant nodes.

Nexus files generated by one program are sometimes incompatible with others. So I read in the fasta file directly:

> data <- readDiscreteCharacterData("ITScombined.aligned.fasta")
Error reading file 'ITScombined.aligned.fasta'
Error:   TaxLabels cannot be repeated. The label BYSTROPOGON_CANARIENSIS has already been stored.
Error:   The error occurred while reading line 0 column 0 in file "ITScombined.aligned.fasta"
Error:  You used a non-model object ( type=NULL ) to create a constant node. Only model objects
can be used for constant nodes.

That gives a clearer error - some of the taxon names are duplicated. They must be unique. Delete the duplicates if you only need one of each, or add a postscript, eg _2, if you want to retain them all.

[hscarter]

I fixed all the duplicated names, but it stills says non model object... Do you have any idea what that problem is?

And thanks, I had a lot of fun last night.

Best, Haley

On Sun, May 1, 2016 at 9:21 AM, Casey Dunn notifications@github.com wrote:

I took a look at JukesCantorITS.Rev to isolate the problem. I executed the commands from the file interactively. Reading in the data matrix gives an error, though it is a bit cryptic:

data <- readDiscreteCharacterData("ITScombined.aligned.nex") Error: You used a non-model object ( type=NULL ) to create a constant node. Only model objects

can be used for constant nodes.

Nexus files generated by one program are sometimes incompatible with others. So I read in the fasta file directly:

data <- readDiscreteCharacterData("ITScombined.aligned.fasta") Error reading file 'ITScombined.aligned.fasta' Error: TaxLabels cannot be repeated. The label BYSTROPOGON_CANARIENSIS has already been stored. Error: The error occurred while reading line 0 column 0 in file "ITScombined.aligned.fasta" Error: You used a non-model object ( type=NULL ) to create a constant node. Only model objects can be used for constant nodes.

That gives a clearer error - some of the taxon names are duplicated. They must be unique. Delete the duplicates if you only need one of each, or add a postscript, eg _2, if you want to retain them all.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/hscarter/phylobio_final_project/issues/1#issuecomment-216041799

[hscarter]

OH MY GOD I GOT IT TO WORK!!!!!! There were two problems. My file was incompatible so I had to export it from Mesquite as a MrBayes NEXUS file instead of just a normal NEXUS file. Then they changed the language to names instead of taxa so I fixed that in my code. Who knows if it will run in time but I'm pretty sure I could fly right now if I tried.