Error while executing the function strict_consensus_merge() in Dendropy 3.12.0.

[Kajori Banerjee]

When I try to merge  the following trees (using scm), I get an error.

tree 1 :   ((((((foo49bar,foo50bar),(foo51bar,(foo33bar,((((((foo32bar,foo31bar),(foo16bar,foo28bar)),foo15bar),foo29bar),((foo24bar,((foo27bar,foo26bar),foo25bar)),(foo14bar,(foo23bar,foo48bar)))),((((foo39bar,(foo38bar,foo37bar)),(foo40bar,(foo12bar,((foo42bar,foo11bar),foo41bar)))),((foo35bar,(foo36bar,foo13bar)),foo34bar)),(((foo46bar,(foo47bar,foo10bar)),(foo45bar,foo44bar)),foo43bar)))))),((((foo52bar,foo53bar),foo54bar),(((foo55bar,(foo17bar,(foo56bar,foo18bar))),((foo57bar,(foo58bar,foo59bar)),foo60bar)),((foo61bar,((foo62bar,(foo63bar,foo19bar)),(foo64bar,(foo65bar,foo66bar)))),(((foo67bar,foo68bar),(foo69bar,(foo20bar,foo70bar))),((foo71bar,foo72bar),foo73bar))))),((foo74bar,(foo75bar,foo76bar)),(((foo77bar,(foo21bar,foo22bar)),(foo78bar,(foo79bar,foo80bar))),((foo81bar,(foo82bar,(foo83bar,foo84bar))),((foo2bar,(foo3bar,foo85bar)),(foo0bar,(foo1bar,foo86bar)))))))),(foo87bar,(foo8bar,(foo88bar,foo9bar)))),foo89bar),foo7bar,foo90bar)

tree 2:  (foo80bar,((((((((((foo67bar,foo68bar),(foo20bar,(foo70bar,foo69bar))),(foo73bar,(foo72bar,foo71bar))),(((foo65bar,foo66bar),((foo19bar,(foo62bar,foo63bar)),foo64bar)),(foo61bar,foo91bar))),((((foo57bar,foo60bar),(foo59bar,foo58bar)),(foo17bar,(foo56bar,foo18bar))),foo55bar)),(foo54bar,(foo52bar,foo53bar))),(foo74bar,(foo76bar,foo75bar))),((foo81bar,((foo83bar,foo84bar),foo82bar)),((foo2bar,(foo85bar,foo3bar)),(foo0bar,(foo86bar,foo1bar))))),foo78bar),((foo21bar,foo22bar),foo77bar)),foo79bar)


Number of leaves in tree1 = 87
Number of leaves in tree2 = 46
Size of intersection =  45

the variable trees is composed of tree1 and tree2
Then I am getting the following error :

File "/projects/tallis/kbanerj3/superfine_b/reup-1.1/reup/adapters.py", line 96, in pairwiseMerger
    output = strict_consensus_merge(trees, gordons_supertree=self.useGordons)
  File "build/bdist.linux-x86_64/egg/dendropy/scm.py", line 316, in strict_consensus_merge
  File "build/bdist.linux-x86_64/egg/dendropy/scm.py", line 343, in inplace_strict_consensus_merge
  File "build/bdist.linux-x86_64/egg/dendropy/scm.py", line 180, in add_to_scm
  File "build/bdist.linux-x86_64/egg/dendropy/scm.py", line 120, in reroot_on_lowest_common_index_path
  File "build/bdist.linux-x86_64/egg/dendropy/dataobject/tree.py", line 1172, in to_outgroup_position
AssertionError


I am using Dendropy 3.12.0. It would be great if you can help me in this regard.

Thanks,
Kajori

[Mark Holder]

Hi,

thanks for the bug report. I'm afraid that I probably won't find time to work on this bug this week. But I will try to fix it next week.

all the best,

mark

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