ETE: cannot connect to X server

[Tianyou96]

Installation process and environment

conda create -n CAFE_fig -c etetoolkit 'ete3==3.0.0b35'
conda list

#
# Name                    Version                   Build  Channel
blas                      1.0                         mkl    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
cairo                     1.14.8                        0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
certifi                   2016.2.28                py35_0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
ete3                      3.0.0b35                 py35_0    http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
fontconfig                2.12.1                        3    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
freetype                  2.5.5                         2    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
glib                      2.50.2                        1    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
harfbuzz                  0.9.39                        2    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libffi                    3.2.1                         1    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libgfortran               3.0.0                         1    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libiconv                  1.14                          0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libpng                    1.6.30                        1    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libxml2                   2.9.4                         0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libxslt                   1.1.29                        0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
lxml                      3.8.0                    py35_0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
mkl                       2017.0.3                      0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
numpy                     1.13.1                   py35_0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
openssl                   1.0.2l                        0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pango                     1.40.3                        1    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pcre                      8.39                          1    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pip                       9.0.1                    py35_1    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pixman                    0.34.0                        0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pyqt                      4.11.4                   py35_4    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
python                    3.5.4                         0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
qt                        4.8.7                         4    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
readline                  6.2                           2    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
scipy                     0.19.1              np113py35_0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
setuptools                36.4.0                   py35_1    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
sip                       4.18                     py35_0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
six                       1.10.0                   py35_0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
sqlite                    3.13.0                        0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
tk                        8.5.18                        0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
wheel                     0.29.0                   py35_0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
xz                        5.2.3                         0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free
zlib                      1.2.11                        0    http://mirrors.ustc.edu.cn/anaconda/pkgs/free

I tried the command:

python3 ./CAFE_fig.py example_result.cafe -c Isoptera=zne,mna -pb 0.05 -pf 0.05 --dump test/ -g .pdf --count_all_expansions
Parsing CAFE report... done!
        Writing test/summary.pdf
ETE: cannot connect to X server

[merondun]

For anyone else running into this issue on an HPC, try to run headless:

mamba create -n cafe_fig -c bioconda -c conda-forge -c etetoolkit 'ete3==3.0.0b35' qt=4 pyqt=4.11.4
mamba activate cafe_fig
wget https://raw.githubusercontent.com/LKremer/CAFE_fig/refs/heads/master/CAFE_fig.py
wget https://raw.githubusercontent.com/LKremer/CAFE_fig/refs/heads/master/example_result.cafe
xvfb-run -a python3 CAFE_fig.py example_result.cafe -pb 0.05 -pf 0.05 --dump test/ -g png --count_all_expansions