problem running beast

[Oscar Godoy Research]

Hi Will, 

I am playing with phylogenerator. It seems a very nice tool that can be used for teaching. Congrats!

However, when I ask phylogenerator to use BEAST with the default settings. I encounter the following problem. I think it is related to phyton rather than phylogenerator but any advice on this would be highly appreciated. 

I am running on Mac. Used four sequences (5.8S, matK, rbcL, trnL) for 16 plant species and two more as outgroup. I imposed a phylogenetic tree constrain obtained from phylomatic in newick format. Each sequence was already aligned using Geneious. To reproduce the problem, all this information is attached. 

Thanks!

Oscar

Phylogeny Building (BEAST - default GTR-GAMMA-chainLength=1000000): 

...running BEAST with default options

...running BEAST with options  BEAST-GTR-GAMMA

/Users/oscargodoy/Desktop/phyloGeneratorMac_1-3-rc/phyloGenerator.app/Contents/Resources/lib/python2.7/site-packages.zip/Bio/Seq.py:341: BiopythonDeprecationWarning: This method is obsolete; please use str(my_seq) instead of my_seq.tostring().

...removing burn-in of  10.0 %...

SKIPPING RATE SMOOTHING STEP

(unecessary with BEAST phylogeny)

Traceback (most recent call last):

  File "/Users/oscargodoy/Desktop/phyloGeneratorMac_1-3-rc/phyloGenerator.app/Contents/Resources/__boot__.py", line 331, in <module>

    _run()

  File "/Users/oscargodoy/Desktop/phyloGeneratorMac_1-3-rc/phyloGenerator.app/Contents/Resources/__boot__.py", line 322, in _run

    exec(compile(source, path, 'exec'), globals(), globals())

  File "/Users/oscargodoy/Desktop/phyloGeneratorMac_1-3-rc/phyloGenerator.app/Contents/Resources/phyloGenerator.py", line 4122, in <module>

    main()

  File "/Users/oscargodoy/Desktop/phyloGeneratorMac_1-3-rc/phyloGenerator.app/Contents/Resources/phyloGenerator.py", line 4099, in main

    currentState.writeOutput()

  File "/Users/oscargodoy/Desktop/phyloGeneratorMac_1-3-rc/phyloGenerator.app/Contents/Resources/phyloGenerator.py", line 3680, in writeOutput

    os.rename(self.oldDirectory + '/' + self.phylogeny, self.stem+"_"+self.geneNames()[i]+"_phylogeny.nex")

OSError: [Errno 2] No such file or directory

2018-02-07 09:28:56.058 phyloGenerator[10910:230703] phyloGenerator Error

[Will]

Hello Oscar,

Thanks for this, and I'm sorry you're having trouble with the program.

Let me start by cutting to the chase and giving you two options you can use right now to get you what you want. (1) use phyloGenerator 2, which runs on Windows, Mac, and Linux and is much faster than pG 1 (http://willpearse.github.io/phyloGenerator2/). (2) Use pez::congeneric.merge, which will give you a phylogeny for your species in a few seconds. In your case, the following lines:

# Load pez

library(pez)

# Load Zanne et al. (2014) phylogeny - DOI:10.1038/nature12872

tree <- read.tree("https://github.com/willpearse/pd_app/raw/master/Vascular_Plants_rooted.dated.tre")

# Load your species list

species <- c("Silene_gallica","Uropappus_lindleyi","Lasthenia_californica","Chaenactis_sp","Centaurea_melitensis","Micropus_californicus","Amsinckia_menziesii","Plantago_sp","Salvia_sp","Euphorbia_sp","Acmispon_sp","Clarkia_bottae","Clarkia_xantiana","Erodium_cicutarium","Erodium_moschatum","Vulpia_microstachys","Magnolia_grandiflora","Amborella_trichopoda")

# Build tree

tree <- congeneric.merge(tree, species)

tree <- drop.tip(tree, setdiff(tree$tip.label, species))

...will give you the tree you're after.

Thank you for reporting this error in so much detail. I'm sad to say that I can reproduce it, and so I may have to release a new version of the program. I hope you can bear with me while I do this; the hardest part of pG was getting it working on Mac, Windows, and Linux because pG contains multiple programs within itself, each of which are a nightmare to get working together. I first released pG in 2012; all of the docker/container solutions we now use for these kinds of problems didn't exist then, so while I think this is an easy fix for the code, it's difficult for me to install all the programs and then bundle them inside pG.

Thanks again for your patience, and I'm sorry this has happened to you. If the fixes I suggest above don't work for you (e.g., you've sent me a 'minimum working example' and need a more complex tree), then please send me another email and I'll work something out for you.

Thanks again,

Will

---

Need a phylogeny? Try phyloGenerator: original or new version

Measuring phylogenetic structure? Try install.packages('pez')

Will Pearse
Assistant Professor of Biology, Utah State University

Office: +1-435-797-0831; Room BR-139

Skype: will.pearse

[Oscar Godoy]

Thanks Will for your prompt and detailed response,

I completely understand the huge effort it takes to make this program work in several platforms. My apologies for making you work harder and I hope you release a new version soon enough.

Meanwhile, I will try pG2! and I will write back to you in case I can not make it work. 

Many thanks,

Oscar

[Will]

Hello Oscar,

Please don't apologise; I'm the one who's written the thing with the bug - I'm very grateful you found it!

Thanks again, and more soon,

Will

---

Need a phylogeny? Try phyloGenerator: original or new version

Measuring phylogenetic structure? Try install.packages('pez')

Will Pearse
Assistant Professor of Biology, Utah State University

Office: +1-435-797-0831; Room BR-139

Skype: will.pearse