# LEfSe after QIIME2 to test at all taxonomic levels

**URL:** https://forum.qiime2.org/t/lefse-after-qiime2-to-test-at-all-taxonomic-levels/15462
**Category:** Other Bioinformatics Tools
**Created:** [June 23, 2020, 10:08pm UTC](https://forum.qiime2.org/t/lefse-after-qiime2-to-test-at-all-taxonomic-levels/15462 "2020-06-23T22:08:28Z")
**Posts on this page:** 1
**Showing post:** 7

<div class="post-metadata">

### Author: ![sbslee](https://forum.qiime2.org/user_avatar/forum.qiime2.org/sbslee/32/9039_2.png) [@sbslee](https://forum.qiime2.org/u/sbslee)
#### Post date: [February 13, 2021, 1:52am UTC](https://forum.qiime2.org/t/lefse-after-qiime2-to-test-at-all-taxonomic-levels/15462/7 "2021-02-13T01:52:04Z")

</div>

@MiriamGorostidi,

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Secondly, you may have one or more outdated libraries installed in your LEfSe environment.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?

```auto
(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?

> [@sbslee](#):
>
> ```auto
> $ dokdo prepare-lefse \
> -t data/moving-pictures-tutorial/table.qza \
> -x data/moving-pictures-tutorial/taxonomy.qza \
> -m data/moving-pictures-tutorial/sample-metadata.tsv \
> -o output/Useful-Information/input_table.tsv \
> -c body-site \
> -u subject \
> -w "[body-site] IN ('tongue', 'gut', 'left palm')"
> 
> ```

---

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