First of all, it seems like you were able to run lefse-plot_res.py without any issues at least and the error is coming from lefse-plot_cladogram.py. Can you confirm this? For example, can you show me the output/Useful-Information/output.pdf file?
Secondly, you may have one or more outdated libraries installed in your LEfSe environment. Can you show me the result of conda list after activating your LEfSe environment?
(lefse) sbslee@x86_64-apple-darwin13 ~ % conda list
# packages in environment at /Users/sbslee/opt/anaconda3/envs/lefse:
#
# Name Version Build Channel
_r-mutex 1.0.1 anacondar_1 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
backports_abc 0.5 py_1 conda-forge
biom-format 2.1.7 py27_0 bioconda
bwidget 1.9.14 h694c41f_0 conda-forge
bzip2 1.0.8 hc929b4f_4 conda-forge
ca-certificates 2020.12.5 h033912b_0 conda-forge
cairo 1.16.0 h0ab9d94_1001 conda-forge
cctools_osx-64 949.0.1 h2f0f38f_19 conda-forge
certifi 2019.11.28 py27h8c360ce_1 conda-forge
clang 11.0.1 h694c41f_1 conda-forge
clang-11 11.0.1 default_hf8bb9ca_1 conda-forge
clang_osx-64 11.0.1 hb91bd55_0 conda-forge
clangxx 11.0.1 default_hf8bb9ca_1 conda-forge
clangxx_osx-64 11.0.1 h7e1b574_0 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
compiler-rt 11.0.1 h654b07c_0 conda-forge
compiler-rt_osx-64 11.0.1 h8c5fa43_0 conda-forge
curl 7.68.0 h8754def_0 conda-forge
cycler 0.10.0 py_2 conda-forge
fontconfig 2.13.1 h1027ab8_1000 conda-forge
freetype 2.10.4 h4cff582_1 conda-forge
fribidi 1.0.10 hbcb3906_0 conda-forge
functools32 3.2.3.2 py_3 conda-forge
future 0.18.2 py27h8c360ce_1 conda-forge
futures 3.3.0 py27h8c360ce_1 conda-forge
gettext 0.19.8.1 haf92f58_1004 conda-forge
gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge
glib 2.66.3 h519c658_0 conda-forge
graphite2 1.3.13 h2e338ed_1001 conda-forge
gsl 2.4 ha2d443c_1006 conda-forge
h5py 2.10.0 nompi_py27h106b333_102 conda-forge
harfbuzz 2.4.0 h92b87b8_1 conda-forge
hdf5 1.10.5 nompi_h0cbb7df_1103 conda-forge
icu 58.2 h0a44026_1000 conda-forge
jpeg 9d hbcb3906_0 conda-forge
kiwisolver 1.1.0 py27h5cd23e5_1 conda-forge
krb5 1.16.4 h1752a42_0 conda-forge
ld64_osx-64 530 hea264c1_19 conda-forge
ldid 2.1.2 h7660a38_2 conda-forge
lefse 1.0.8.post1 py27_2 bioconda
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libclang-cpp11 11.0.1 default_hf8bb9ca_1 conda-forge
libcurl 7.68.0 h709d2b2_0 conda-forge
libcxx 11.0.1 habf9029_0 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libffi 3.2.1 hb1e8313_1007 conda-forge
libgfortran 3.0.1 0 conda-forge
libglib 2.66.3 h2575888_0 conda-forge
libiconv 1.16 haf1e3a3_0 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libllvm11 11.0.1 h223d4b2_0 conda-forge
libopenblas 0.3.7 hd44dcd8_1 conda-forge
libpng 1.6.37 h7cec526_2 conda-forge
libssh2 1.9.0 h8a08a2b_5 conda-forge
libtiff 4.2.0 h355d032_0 conda-forge
libwebp-base 1.1.0 hbcb3906_3 conda-forge
libxml2 2.9.9 hd80cff7_2 conda-forge
linecache2 1.0.0 py_1 conda-forge
llvm-openmp 11.0.1 h7c73e74_0 conda-forge
llvm-tools 11.0.1 h223d4b2_0 conda-forge
lz4-c 1.9.3 h046ec9c_0 conda-forge
make 4.3 h22f3db7_1 conda-forge
matplotlib 2.1.2 py27_1 conda-forge
matplotlib-base 2.1.2 py27h31f9439_1 conda-forge
ncurses 6.2 h2e338ed_4 conda-forge
numpy 1.16.5 py27hde6bac1_0 conda-forge
openssl 1.1.1i h35c211d_0 conda-forge
pandas 0.24.2 py27h86efe34_0 conda-forge
pango 1.42.4 haa940fe_4 conda-forge
pcre 8.44 hb1e8313_0 conda-forge
pip 20.1.1 pyh9f0ad1d_0 conda-forge
pixman 0.38.0 h01d97ff_1003 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqi 0.3.2 py27_1 bioconda
python 2.7.15 h8e446fc_1011_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 2.7 1_cp27m conda-forge
pytz 2020.1 pyh9f0ad1d_0 conda-forge
r-base 3.5.3 hb1347aa_0
r-codetools 0.2_16 r35h6115d3f_1001 conda-forge
r-coin 1.3_1 r35h159158b_0 conda-forge
r-lattice 0.20_41 r35h17f1fa6_1 conda-forge
r-libcoin 1.0_5 r35h26f5615_1 conda-forge
r-mass 7.3_51.6 r35h17f1fa6_1 conda-forge
r-matrix 1.2_18 r35h26f5615_2 conda-forge
r-matrixstats 0.56.0 r35h17f1fa6_0 conda-forge
r-modeltools 0.2_23 r35h6115d3f_0 conda-forge
r-multcomp 1.4_13 r35h6115d3f_0 conda-forge
r-mvtnorm 1.0_11 r35haf69682_2 conda-forge
r-sandwich 2.5_1 r35h6115d3f_1 conda-forge
r-survival 3.1_12 r35h17f1fa6_0 conda-forge
r-th.data 1.0_10 r35h6115d3f_1 conda-forge
r-zoo 1.8_7 r35h17f1fa6_0 conda-forge
readline 8.0 h0678c8f_2 conda-forge
rpy2 2.8.6 py27r35hfc83f80_2 conda-forge
scipy 1.2.1 py27hab3da7d_2 conda-forge
setuptools 44.0.0 py27_0 conda-forge
singledispatch 3.4.0.3 pyh9f0ad1d_1001 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sqlite 3.34.0 h17101e1_0 conda-forge
subprocess32 3.5.4 py27h0b31af3_0 conda-forge
tapi 1100.0.11 h9ce4665_0 conda-forge
tk 8.6.10 h0419947_1 conda-forge
tktable 2.10 h49f0cf7_3 conda-forge
tornado 5.1.1 py27h1de35cc_1000 conda-forge
traceback2 1.4.0 py27_0 conda-forge
unittest2 1.1.0 py_0 conda-forge
wheel 0.36.2 pyhd3deb0d_0 conda-forge
xz 5.2.5 haf1e3a3_1 conda-forge
zlib 1.2.11 h7795811_1010 conda-forge
zstd 1.4.8 hf387650_1 conda-forge
(lefse) sbslee@x86_64-apple-darwin13 ~ %
Finally, can you make sure you are using the exact input files in the tutorial?