Errors with generating tree with ControlFileGenerator

[FatihSarigol]

Hello again,
I am trying to use my newick tree with the ControlFileGenerator and I don't understand the rules here. When I type in the example tree it works, but my tree which comes from a FigTree export and also works on treeview of etoolkit without an issue gives error with your program:

((((Norway,NPresident),NPtransient),SouthAfrican),Antarctic,MarionIsland)

It says "Errors in the tree input" "Last character can't be a braket or a comma"

When I add ";" or "root" to the end, it then says "Error: Check your commas"

Can you see a reason what may be causing the error?
Thanks!

[gphocs-dev]

Sorry for the delayed response. you're supposed to name the ancestral nodes in the tree (these are the ancestral populations in your phylogeny), and you also have to have a root. Your Newick tree had a 3-way split at the root. This version works:
(((((Norway,NPresident)ANC1,NPtransient)ANC2,SouthAfrican)ANC3,Antarctic)ANC4,MarionIsland)ROOT

This version assumes that Antarctic and MarionIsland are not sister populations.

[FatihSarigol]

Thank you for your reply!
We also ended up trying that actually ourselves and it did work!

I don't want to open a new thread for the following, and I believe I have fixed them myself, but 2 more issues with using a control file generated by ControlFileGenerator. When I used the control file, it gave this error:

.rror: value of const-rate should be CONST, FIXED, or VAR, got CONST
'.ror: value of find-finetunes should be TRUE or FALSE, got 'TRUE
Found 2 errors when parsing GENERAL-INFO in control file testX.

In the control file these 2 lines it doesn't like are as below:

            find-finetunes          TRUE
            locus-mut-rate          CONST

So, probably an issue regarding an empty character more or a newline character less or the order of the lines, I couldn't get to the bottom of that. I used the ControlFileGenerator in Windows 7 and I copied the control file it generated directly to my unix environment without opening it in Windows (I mean the file was not edited anywhere afterwards). So I used the GENERAL-INFO part from the example sample-control-file.ctl after editing for my case.

And the next error was this:

Error: uneven terms in sample line for pop 1.
Error: expecting to see 2 samples in pop 1, but was able to read only 3.
Error: uneven terms in sample line for pop 2.
Error: expecting to see 2 samples in pop 2, but was able to read only 3.
Error: uneven terms in sample line for pop 3.
Error: expecting to see 2 samples in pop 3, but was able to read only 3.
Error: uneven terms in sample line for pop 4.
Error: expecting to see 2 samples in pop 4, but was able to read only 3.
Error: uneven terms in sample line for pop 5.
Error: expecting to see 2 samples in pop 5, but was able to read only 3.
Error: uneven terms in sample line for pop 6.
Segmentation fault

I compared the control file generated by ControlFileGenerator with the example control file and noticed that the generated one had either a space or a tab after the "d" for each samples line of each population. Here is an example:

            POP-START
                            name            Norway
                            samples         Norway d 
            POP-END

Here it is not so informative, but after "Norway d" there is a space that Gphocs thinks it is a third sample and gives an error. I deleted those for each sample and it worked.

Best..

[gphocs-dev]

All of these errors appear to stem from the fact that you're generating the control file on Windows (in the Control File Generator) and then using it on a Linux machine. When you transfer text files between Windows and Linux you have to use a special converter to switch the newline characters (e.g. dos2unix). Because the newline characters are differernt, G-PhoCS cannot successfully read the last token of every line.