Can't build consensus tree on bootstrap files from RAxML - trees with singleton nodes?

[Marek Borowiec]

Hello,

I have multiple files with 200 bootstrap trees from RAxML runs and I'm trying to make a consensus tree for each file, collapsing nodes below a certain threshold, say 75.

I'm calling raxml with the following (embedded in a bash loop):

raxml -T 3 -m PROTGAMMAAUTO -J T_75  -z $FILE -n $FILE.CONS_75

This works for some files, but for most I get output with an error (see below). I tried to work around this problem by making consensus trees using R's ape and phytools, but they trip on the same files. After some research I found this discussion of singleton nodes at Liam Revell's blog. I think this may be the problem with my trees, because of the same R error I'm getting trying to process these files. 

I'm attaching two files: one that works and one that doesn't. I'm using RAxML v8.1.3.

I appreciate your help.

Best,

Marek Borowiec

Example of failed run:

RAxML was called as follows:

raxml -T 3 -m PROTGAMMAAUTO -J T_75 -z RAxML_bootstrap.OG9.OUT -n RAxML_bootstrap.OG9.OUT.CONS_75 

Found 200 trees in File RAxML_bootstrap.OG9.OUT

ERROR: Expecting ';' at end of tree; found: character ','

)),Mnemiopsis))))))),Tetranychus,Daphnia

                    ^

RAxML may be expecting to read a tree that contains branch lengths

raxml: treeIO.c:2256: readMultifurcatingTree: Assertion `0' failed.

[Alexandros Stamatakis]

Hi Marek,

Can you please send me the input files?

How exactly did you assemble the trees -z $FILE?

Is this just the RAxML_bootstrap file or did you do some editing or
file-merging before passing the tree set file to RAxML?

Cheers,

Alexis

> I have multiple files with 200 bootstrap trees from RAxML runs and I'm
> trying to make a consensus tree for each file, collapsing nodes below a
> certain threshold, say 75.
>
> I'm calling raxml with the following (embedded in a bash loop):
>
> raxml -T 3 -m PROTGAMMAAUTO -J T_75 -z $FILE -n $FILE.CONS_75
>
> This works for some files, but for most I get output with an error (see
> below). I tried to work around this problem by making consensus trees using
> R's ape and phytools, but they trip on the same files. After some research
> I found this discussion of singleton nodes at Liam Revell's blog

> <http://blog.phytools.org/2013/06/robust-newick-tree-reader.html>. I think

> this may be the problem with my trees, because of the same R error I'm
> getting trying to process these files.
>
> I'm attaching two files: one that works and one that doesn't. I'm using
> RAxML v8.1.3.
>
> I appreciate your help.
>
> Best,
> Marek Borowiec
>
>
> Example of failed run:
>
> RAxML was called as follows:
>
> raxml -T 3 -m PROTGAMMAAUTO -J T_75 -z RAxML_bootstrap.OG9.OUT -n
> RAxML_bootstrap.OG9.OUT.CONS_75
>
> Found 200 trees in File RAxML_bootstrap.OG9.OUT
>
> ERROR: Expecting ';' at end of tree; found: character ','
>
> )),Mnemiopsis))))))),Tetranychus,Daphnia
> ^
>
> RAxML may be expecting to read a tree that contains branch lengths
>
> raxml: treeIO.c:2256: readMultifurcatingTree: Assertion `0' failed.
>
>

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Marek Borowiec]

Dear Alexis,

I apologize for the trouble. I think I must have accidentally corrupted some of the bootstrap files by removing opening bracket when using recursive sed intended to modify some other files. I just appended a bracket to all corrupted files and this solved the problem.

[Alexandros Stamatakis]

:-)

alexis

On 28.10.2014 01:35, Marek Borowiec wrote:
> Dear Alexis,
>
> I apologize for the trouble. I think I must have accidentally corrupted
> some of the bootstrap files by removing opening bracket when using
> recursive sed intended to modify some other files. I just appended a
> bracket to all corrupted files and this solved the problem.
>
> On Saturday, October 25, 2014 3:05:48 PM UTC-7, Marek Borowiec wrote:
>>
>> Hello,
>>
>> I have multiple files with 200 bootstrap trees from RAxML runs and I'm
>> trying to make a consensus tree for each file, collapsing nodes below a
>> certain threshold, say 75.
>>
>> I'm calling raxml with the following (embedded in a bash loop):
>>
>> raxml -T 3 -m PROTGAMMAAUTO -J T_75 -z $FILE -n $FILE.CONS_75
>>
>> This works for some files, but for most I get output with an error (see
>> below). I tried to work around this problem by making consensus trees using
>> R's ape and phytools, but they trip on the same files. After some research
>> I found this discussion of singleton nodes at Liam Revell's blog

>> <http://blog.phytools.org/2013/06/robust-newick-tree-reader.html>. I

>> think this may be the problem with my trees, because of the same R error
>> I'm getting trying to process these files.
>>
>> I'm attaching two files: one that works and one that doesn't. I'm using
>> RAxML v8.1.3.
>>
>> I appreciate your help.
>>
>> Best,
>> Marek Borowiec
>>
>>
>> Example of failed run:
>>
>> RAxML was called as follows:
>>
>> raxml -T 3 -m PROTGAMMAAUTO -J T_75 -z RAxML_bootstrap.OG9.OUT -n
>> RAxML_bootstrap.OG9.OUT.CONS_75
>>
>> Found 200 trees in File RAxML_bootstrap.OG9.OUT
>>
>> ERROR: Expecting ';' at end of tree; found: character ','
>>
>> )),Mnemiopsis))))))),Tetranychus,Daphnia
>> ^
>>
>> RAxML may be expecting to read a tree that contains branch lengths
>>
>> raxml: treeIO.c:2256: readMultifurcatingTree: Assertion `0' failed.
>>
>>
>>
>