What format are GTDB-Tk newick trees and how to extract specific node?

Question

[O.rka]

I'm trying to read my tree from the classify/ directory from GTDB-Tk but I'm getting an error:

In [50]: tree = ete3.Tree("./classify/gtdbtk.bac120.classify.tree", format=0, quoted_node_names=True)
---------------------------------------------------------------------------
NewickError                               Traceback (most recent call last)
<ipython-input-50-913e9702b09b> in <module>
----> 1 tree = ete3.Tree("./classify/gtdbtk.bac120.classify.tree", format=0, quoted_node_names=True)

/usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/soothsayer_py3.8_env/lib/python3.8/site-packages/ete3/coretype/tree.py in __init__(self, newick, format, dist, support, name, quoted_node_names)
    208         if newick is not None:
    209             self._dist = 0.0
--> 210             read_newick(newick, root_node = self, format=format,
    211                         quoted_names=quoted_node_names)
    212

/usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/soothsayer_py3.8_env/lib/python3.8/site-packages/ete3/parser/newick.py in read_newick(newick, root_node, format, quoted_names)
    249             raise NewickError('Unexisting tree file or Malformed newick tree structure.')
    250         else:
--> 251             return _read_newick_from_string(nw, root_node, matcher, format, quoted_names)
    252
    253     else:

/usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/soothsayer_py3.8_env/lib/python3.8/site-packages/ete3/parser/newick.py in _read_newick_from_string(nw, root_node, matcher, formatcode, quoted_names)
    324                     closing_internal =  closing_internal.rstrip(";")
    325                     # read internal node data and go up one level
--> 326                     _read_node_data(closing_internal, current_parent, "internal", matcher, formatcode)
    327                     current_parent = current_parent.up
    328

/usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/soothsayer_py3.8_env/lib/python3.8/site-packages/ete3/parser/newick.py in _read_node_data(subnw, current_node, node_type, matcher, formatcode)
    428             _parse_extra_features(node, data[2])
    429     else:
--> 430         raise NewickError("Unexpected newick format '%s' " %subnw[0:50])
    431     return
    432

NewickError: Unexpected newick format 'ete3_quotref_1:0.09438'
You may want to check other newick loading flags like 'format' or 'quoted_node_names'.

I was able to successfully read using format=1 but I'm getting nodes with the name 1.0 which I don't think is correct:

In [49]: p_node.get_common_ancestor(["MAG_883.8", "MAG_883.14"])
Out[49]: Tree node '1.0' (0x7f810794d82)