RogueNaRok crashing with some trees: "ERROR: Expecting ')' in tree; found:"

[Simon Uribe-Convers]

Hi All,

I have a a set of 583 gene trees (different genes) and I managed to make them have the same exact taxa so that RogueNaRok could work on them. However, I started to see an error when running the program:

"

RogueNaRok -T 8 -i All_Trees_Inclusive_Data_test.trees -n test -w .

This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011-10-25.

Found a total of 59 taxa in first tree of tree collection All_Trees_Inclusive_Data_test.trees

Expecting all remaining trees in collection to have the same taxon set

mode: optimization on consensus tree. Bipartition is part of consensus, if it occurs in more than 149 trees

ERROR: Expecting ')' in tree; found:,Burmeistera_vulgaris_2016_100_Combined:

ERROR: Expecting ')' in tree; found:0.0):0.00055,Burmeistera_draconis_2016_1

ERROR: Expecting ';' at end of tree; found:)0.257:0.00140)0.892:0.00401,LL6_C_smith

ERROR: Unable to uproot tree.  Inconsistent

       number of tips and nodes for rooted tree.

Segmentation fault: 11

"

After a bit of searching,  I found a similar thread on RAxML (here) and the root of the problem was that not all trees were fully bifurcating. I checked if my tree were and of course they weren't! After forcing them to be, R code below, RogueNaRok worked great. 

More than a problem I need help with, I'm writing this post so that other people in the future can find a reference to the problem. The requirement of fully bifurcating trees is not described in the manual or the wiki page (probably because this is meant to be used with RAxML trees from a single locus that won't have polytomies) but maybe it would be a nice addition to the documentation.

Thanks for the great program!

Best,

Simon

#R code for fully bifurcating trees for a multiphylo object 

```

for(i in 1:length(tree)) {

tre<-multi2di(tree[[i]])

write.tree(tre, file="Your_Fully_Bifurcating.trees", append=TRUE)

}

```

[Alexandros Stamatakis]

Dear Simon,

Thanks a million, I'd wish more users would be doing that, I've updated
the wiki following your suggestion.

All the best,

Alexis

On 08.07.2017 14:42, Simon Uribe-Convers wrote:
> Hi All,
>
> I have a a set of 583 gene trees (different genes) and I managed to make
> them have the same exact taxa so that RogueNaRok could work on them.
> However, I started to see an error when running the program:
>
> "
> RogueNaRok -T 8 -i All_Trees_Inclusive_Data_test.trees -n test -w .
>
> This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011-10-25.
>
> Found a total of 59 taxa in first tree of tree collection
> All_Trees_Inclusive_Data_test.trees
> Expecting all remaining trees in collection to have the same taxon set
>
> mode: optimization on consensus tree. Bipartition is part of consensus,
> if it occurs in more than 149 trees
> ERROR: Expecting ')' in tree; found:,Burmeistera_vulgaris_2016_100_Combined:
> ERROR: Expecting ')' in tree; found:0.0):0.00055,Burmeistera_draconis_2016_1
> ERROR: Expecting ';' at end of tree;
> found:)0.257:0.00140)0.892:0.00401,LL6_C_smith
> ERROR: Unable to uproot tree. Inconsistent
> number of tips and nodes for rooted tree.
> Segmentation fault: 11
>
> "
>
> After a bit of searching, I found a similar thread on RAxML (here

> <https://groups.google.com/forum/#!topic/raxml/tHe3lcy3QTo>) and the

> root of the problem was that not all trees were fully bifurcating. I
> checked if my tree were and of course they weren't! After forcing them
> to be, R code below, RogueNaRok worked great.
>
> More than a problem I need help with, I'm writing this post so that
> other people in the future can find a reference to the problem. The
> requirement of fully bifurcating trees is not described in the manual or
> the wiki page (probably because this is meant to be used with RAxML
> trees from a single locus that won't have polytomies) but maybe it would
> be a nice addition to the documentation.
>
> Thanks for the great program!
>
> Best,
> Simon
>
>
> #R code for fully bifurcating trees for a multiphylo object
>
> ```
> for(i in 1:length(tree)) {
> tre<-multi2di(tree[[i]])
> write.tree(tre, file="Your_Fully_Bifurcating.trees", append=TRUE)
> }
> ```
>

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org