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neherlab / treetime_examples

A collection of documented examples using TreeTime
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AttributeError: 'module' object has no attribute 'popall' #6

Closed Cactusolo closed 4 years ago

Cactusolo commented 4 years ago

Hi , I have been using TreeTime: Maximum Likelihood Phylodynamics tt 0.7.4, with standard run treetime --tree iqtree_alnclen.tre --aln subiqtree.fasta --dates date_iqtree.csv. It was all good, but giving error as half-way.

The error msg is "AttributeError: 'module' object has no attribute 'popall'" as detailes, below. Any suggestions are appreciated.

Symmetrized rates from j->i (W_ij): A C G T - A 0 0.4601 1.8243 0.6456 7.8015 C 0.4601 0 0.3286 3.7665 8.3047 G 1.8243 0.3286 0 0.6436 6.2111 T 0.6456 3.7665 0.6436 0 7.3774

Actual rates from j->i (Q_ij): A C G T - A 0 0.1361 0.5396 0.191 2.3074 C 0.0819 0 0.0585 0.6703 1.4779 G 0.3503 0.0631 0 0.1236 1.1927 T 0.2094 1.2216 0.2087 0 2.3927

Inferred sequence evolution model (saved as 2020-04-01_treetime/molecular_clock.txt): Root-Tip-Regression: --rate: 9.280e-04 --r^2: 0.32

/home/.local/lib/python2.7/site-packages/matplotlib/colors.py:680: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1. not cbook.is_string_like(colors[0]): /home/.local/lib/python2.7/site-packages/matplotlib/lines.py:44: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1. if is_string_like(style) and is_hashable(style): /home/.local/lib/python2.7/site-packages/matplotlib/font_manager.py:971: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1. if is_string_like(family): /home/.local/lib/python2.7/site-packages/matplotlib/font_manager.py:697: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1. if is_string_like(family): /home/.local/lib/python2.7/site-packages/matplotlib/text.py:218: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1. elif is_string_like(fontproperties): Traceback (most recent call last): File "/usr/local/bin/treetime", line 12, in return_code = params.func(params) File "/usr/local/lib/python2.7/dist-packages/treetime/argument_parser.py", line 213, in toplevel timetree(params) File "/usr/local/lib/python2.7/dist-packages/treetime/wrappers.py", line 607, in timetree confidence=0.9 if calc_confidence else None) File "/usr/local/lib/python2.7/dist-packages/treetime/treetime.py", line 829, in plot_vs_years ax = plt.subplot(111) File "/home/.local/lib/python2.7/site-packages/matplotlib/pyplot.py", line 1044, in subplot a = fig.add_subplot(*args, *kwargs) File "/home/.local/lib/python2.7/site-packages/matplotlib/figure.py", line 1021, in add_subplot a = subplot_class_factory(projection_class)(self, args, kwargs) File "/home/.local/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 73, in init self._axes_class.init(self, fig, self.figbox, kwargs) File "/home/.local/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 529, in init self._init_axis() File "/home/.local/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 622, in _init_axis self.xaxis = maxis.XAxis(self) File "/home/.local/lib/python2.7/site-packages/matplotlib/axis.py", line 676, in init self.cla() File "/home/.local/lib/python2.7/site-packages/matplotlib/axis.py", line 760, in cla self.reset_ticks() File "/home/.local/lib/python2.7/site-packages/matplotlib/axis.py", line 771, in reset_ticks cbook.popall(self.majorTicks) AttributeError: 'module' object has no attribute 'popall'

Miao

Cactusolo commented 4 years ago

OK, it was resolved by sudo apt-get install python-matplotlib. [In case others needed]