cmfl_results.R script error about clonalframeml

[xavierdidelot]

Hi Shane,

I think it worked and you should now have the pdf file in the directory in which you executed the command. You can ignore the warnings. Don't hesitate to reopen this issue if the pdf is not there.

Best wishes,
Xavier

[slhogle]

Hi Xavier,

Thanks for your help! It works fine now that I tried it on my local computer... For some reason when I ran it on our cluster it was not producing the pdf output.

best,
shane

[StephanieRodrigues]

Hi guys,
Do you know if it is possible reorder the tree? I opened the newick tree that ClonalFrame gave me on FigTree and organized and rooted it like I would like to have in my paper. I saved in newick format with the appropriate name to run the R. script but this message appeared:

Error in if (all(phy$node.label == "")) phy$node.label <- NULL :
missing value where TRUE/FALSE needed
Calls: read.tree -> lapply -> FUN
Execution halted

Best
Stephanie

[danny-wilson]

You need to re-root the tree before the ClonalFrameML analysis. best wishes, Danny

…

On Fri, 15 Mar 2019 at 20:46, StephanieRodrigues ***@***.***> wrote: Hi guys, Do you know if it is possible reorder the tree? I opened the newick tree that ClonalFrame gave me on FigTree and organized and rooted it like I would like to have in my paper. I saved in newick format with the appropriate name to run the R. script but this message appeared: Error in if (all(phy$node.label == "")) phy$node.label <- NULL : missing value where TRUE/FALSE needed Calls: read.tree -> lapply -> FUN Execution halted Best Stephanie — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#44 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APKSYIMVnAQ8ycBQXKTbTshtcPsYUmT4ks5vXAa_gaJpZM4KGB5y> .

[StephanieRodrigues]

Hey Danny,
Thank you so much, I had this insight before I go to bed yesterday!
I`ll do this!
best,
Stephanie