Error when creating matrix/exporting trees

[Tom Lawrence]

I can import trees and bibtex files but when trying to export trees or create matrices I get the following error:

Failed to export trees due to an unknown error. Please report this a bug
Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk_gui\interface.py", line 1973, in on_export_trees_save
    output_string = stk.amalgamate_trees(XML,format=format,anonymous=anonymous,ignoreWarnings=False)
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 1392, in amalgamate_trees
    _check_data(XML)
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 3395, in _check_data
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 3331, in _check_taxa
    t.getparent().remove(t)
  File "lxml.etree.pyx", line 2355, in lxml.etree._Attrib.__getitem__ (src\lxml\lxml.etree.c:62162)
KeyError: 'name'

Failed to create matrix due to an unknown error.
Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk_gui\interface.py", line 1722, in on_create_matrix_create_matrix_button
    matrix = stk.create_matrix(XML,format=format,taxonomy=taxonomy_tree,outgroups=no_outgroups,ignoreWarnings=ignoreWarnings)
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 1518, in create_matrix
    _check_data(XML)
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 3395, in _check_data
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 3331, in _check_taxa
    t.getparent().remove(t)
  File "lxml.etree.pyx", line 2355, in lxml.etree._Attrib.__getitem__ (src\lxml\lxml.etree.c:62162)
KeyError: 'name'

Both errors seem to boil down to the lxml.etree.pyx file or the name issue, I have installed lxml via pip but I am still getting the same error.
If I ignore warnings for matrix creation, it saves an output file but this does not work for the export trees function.
Any help in resolving this would be really appreciated.

[Jon Hill (jon-hill)]

Hi Tom,

Thanks for reporting. I suspect this is because you don't have all the information required inputted into the GUI. Can you send/attach the PHYML file and I can take a look? In the GUI everything in blue text should be completed (even with dummy data).