Open druvus opened 4 years ago
Could you give some information about your operating system?
Could you also paste the conda channel order and conda version? You may get that information by the command conda info
Change back to import each function
from ete3 import Tree, faces, AttrFace, TreeStyle, NodeStyle
and instead fix so that conda installation (won´t crashing on importing faces). Related to this issue (https://github.com/etetoolkit/ete/issues/315 ). Requires pyqt (5 or later) to be installed.
@standage I tested the same command as you with the public FSC200 genome and it worked fine
CanSNPer2 --database ~/github/CanSNPer2-data/database/francisella_tularensis.db fasta/FSC200_GCF000168775.2.fna
This is whats in my conda environment. (conda list
) Running conda 4.8.2
# packages in environment at /mnt/powervault/carodl/miniconda3/envs/cansnper2_conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge
cansnper2 2.0.6 py_0 bioconda
certifi 2020.4.5.1 py38h32f6830_0 conda-forge
dbus 1.13.6 he372182_0 conda-forge
ete3 3.1.1 py_1 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
flextaxd 0.2.1 py_0 bioconda
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.1 he06d7ca_0 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
glib 2.64.2 h6f030ca_0 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
icu 64.2 he1b5a44_1 conda-forge
jpeg 9c h14c3975_1001 conda-forge
ld_impl_linux-64 2.34 h53a641e_0 conda-forge
libblas 3.8.0 16_openblas conda-forge
libcblas 3.8.0 16_openblas conda-forge
libclang 9.0.1 default_hde54327_0 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libiconv 1.15 h516909a_1006 conda-forge
liblapack 3.8.0 16_openblas conda-forge
libllvm9 9.0.1 he513fc3_1 conda-forge
libopenblas 0.3.9 h5ec1e0e_0 conda-forge
libpng 1.6.37 hed695b0_1 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.10.0 he1b5a44_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libxslt 1.1.33 h31b3aaa_0 conda-forge
llvm-openmp 10.0.0 hc9558a2_0 conda-forge
lxml 4.5.0 py38hbb43d70_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
nspr 4.25 he1b5a44_0 conda-forge
nss 3.47 he751ad9_0 conda-forge
numpy 1.18.4 py38h8854b6b_0 conda-forge
openssl 1.1.1g h516909a_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pip 20.1 pyh9f0ad1d_0 conda-forge
progressivemauve snapshot_2015_02_13 2 bioconda
pthread-stubs 0.4 h14c3975_1001 conda-forge
pyqt 5.12.3 py38ha8c2ead_2 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtchart 5.12 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
python 3.8.2 he5300dc_7_cpython conda-forge
python_abi 3.8 1_cp38 conda-forge
qt 5.12.5 hd8c4c69_1 conda-forge
readline 8.0 hf8c457e_0 conda-forge
scipy 1.4.1 py38h18bccfc_3 conda-forge
setuptools 46.1.3 py38h32f6830_0 conda-forge
six 1.14.0 py_1 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
wheel 0.34.2 py_1 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.9 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.5 h516909a_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
@standage I´m looking into this issue. It would be great to get some more details about your operating system and installed packages similar to what Caroline posted above. I cannot replicate your problem using default installations in conda.
Sorry for the delayed response, I am trying to catch up after a 3-day holiday weekend.
I am using CentOS 7 and Conda 4.8.3. See my setup below.
I have tried several configurations and methods of installing CanSNPer2 and ETE3 beside what is shown below, but I continue to have issues. I have found some of the issue threads mentioned above, but I confirmed from the Python interpreter that PyQt5 is installed correctly.
(base) [standage@worky ~]$ cat /etc/redhat-release
CentOS Linux release 7.7.1908 (Core)
(base) [standage@worky ~]$ cat ~/.condarc
channels:
- etetoolkit
- bioconda
- conda-forge
- defaults
(base) [standage@worky ~]$ conda create --name cansnper2 -y cansnper2
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/standage/anaconda3/envs/cansnper2
added / updated specs:
- cansnper2
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm
binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_2
ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0
cansnper2 bioconda/noarch::cansnper2-2.0.6-py_0
certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0
dbus conda-forge/linux-64::dbus-1.13.6-he372182_0
ete3 etetoolkit/noarch::ete3-3.1.1-pyhf5214e1_0
expat conda-forge/linux-64::expat-2.2.9-he1b5a44_2
flextaxd bioconda/noarch::flextaxd-0.2.1-py_0
fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001
freetype conda-forge/linux-64::freetype-2.10.2-he06d7ca_0
gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.5.0-hd420e75_6
gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.5.0-hdf63c60_6
glib conda-forge/linux-64::glib-2.64.3-h6f030ca_0
gst-plugins-base conda-forge/linux-64::gst-plugins-base-1.14.5-h0935bb2_2
gstreamer conda-forge/linux-64::gstreamer-1.14.5-h36ae1b5_2
gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.5.0-hdf63c60_6
icu conda-forge/linux-64::icu-64.2-he1b5a44_1
jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_2
libblas conda-forge/linux-64::libblas-3.8.0-16_openblas
libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas
libclang conda-forge/linux-64::libclang-9.0.1-default_hde54327_0
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_6
libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2
libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006
liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas
libllvm9 conda-forge/linux-64::libllvm9-9.0.1-he513fc3_1
libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0
libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2
libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002
libxkbcommon conda-forge/linux-64::libxkbcommon-0.10.0-he1b5a44_0
libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0
libxslt conda-forge/linux-64::libxslt-1.1.33-h31b3aaa_0
llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0
lxml conda-forge/linux-64::lxml-4.5.1-py38hbb43d70_0
ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
nspr conda-forge/linux-64::nspr-4.25-he1b5a44_0
nss conda-forge/linux-64::nss-3.47-he751ad9_0
numpy conda-forge/linux-64::numpy-1.18.4-py38h8854b6b_0
openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0
pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0
pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
progressivemauve bioconda/linux-64::progressivemauve-snapshot_2015_02_13-2
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
pyqt conda-forge/linux-64::pyqt-5.12.3-py38ha8c2ead_3
python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython
python_abi conda-forge/linux-64::python_abi-3.8-1_cp38
qt conda-forge/linux-64::qt-5.12.5-hd8c4c69_1
readline conda-forge/linux-64::readline-8.0-hf8c457e_0
scipy conda-forge/linux-64::scipy-1.4.1-py38h18bccfc_3
setuptools conda-forge/linux-64::setuptools-46.4.0-py38h32f6830_0
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0
sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-h3a0023d_3
tk conda-forge/linux-64::tk-8.6.10-hed695b0_0
wheel conda-forge/noarch::wheel-0.34.2-py_1
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_0
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate cansnper2
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) [standage@worky ~]$ conda activate cansnper2
(cansnper2) [standage@worky ~]$ conda list
# packages in environment at /home/standage/anaconda3/envs/cansnper2:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
binutils_impl_linux-64 2.34 h53a641e_2 conda-forge
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge
cansnper2 2.0.6 py_0 bioconda
certifi 2020.4.5.1 py38h32f6830_0 conda-forge
dbus 1.13.6 he372182_0 conda-forge
ete3 3.1.1 pyhf5214e1_0 etetoolkit
expat 2.2.9 he1b5a44_2 conda-forge
flextaxd 0.2.1 py_0 bioconda
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.2 he06d7ca_0 conda-forge
gcc_impl_linux-64 7.5.0 hd420e75_6 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
gfortran_impl_linux-64 7.5.0 hdf63c60_6 conda-forge
glib 2.64.3 h6f030ca_0 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
gxx_impl_linux-64 7.5.0 hdf63c60_6 conda-forge
icu 64.2 he1b5a44_1 conda-forge
jpeg 9c h14c3975_1001 conda-forge
ld_impl_linux-64 2.34 h53a641e_2 conda-forge
libblas 3.8.0 16_openblas conda-forge
libcblas 3.8.0 16_openblas conda-forge
libclang 9.0.1 default_hde54327_0 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.5.0 hdf63c60_6 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libiconv 1.15 h516909a_1006 conda-forge
liblapack 3.8.0 16_openblas conda-forge
libllvm9 9.0.1 he513fc3_1 conda-forge
libopenblas 0.3.9 h5ec1e0e_0 conda-forge
libpng 1.6.37 hed695b0_1 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.10.0 he1b5a44_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libxslt 1.1.33 h31b3aaa_0 conda-forge
llvm-openmp 10.0.0 hc9558a2_0 conda-forge
lxml 4.5.1 py38hbb43d70_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
nspr 4.25 he1b5a44_0 conda-forge
nss 3.47 he751ad9_0 conda-forge
numpy 1.18.4 py38h8854b6b_0 conda-forge
openssl 1.1.1g h516909a_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pip 20.1.1 pyh9f0ad1d_0 conda-forge
progressivemauve snapshot_2015_02_13 2 bioconda
pthread-stubs 0.4 h14c3975_1001 conda-forge
pyqt 5.12.3 py38ha8c2ead_3 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtchart 5.12 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
python 3.8.2 he5300dc_7_cpython conda-forge
python_abi 3.8 1_cp38 conda-forge
qt 5.12.5 hd8c4c69_1 conda-forge
readline 8.0 hf8c457e_0 conda-forge
scipy 1.4.1 py38h18bccfc_3 conda-forge
setuptools 46.4.0 py38h32f6830_0 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
sysroot_linux-64 2.12 h3a0023d_3 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
wheel 0.34.2 py_1 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xz 5.2.5 h516909a_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
If I run the same step without the etetoolkit
channel in my ~/.condarc
, it installs Python 3.6 instead of Python 3.8 but I still get the same runtime error with ete3.NodeStyle()
.
Thank you @standage
I am trying to recreate your bug, would it be possible for you to try ete3 directly in python to see if we can pinpoint the problem.
What happens if you run the command ete3.NodeStyle() in a python terminal after importing ete3?
python Python 3.8.2 | packaged by conda-forge | (default, Mar 5 2020, 17:11:00) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.
import ete3 ete3.NodeStyle() {'fgcolor': '#0030c1', 'bgcolor': '#FFFFFF', 'vt_line_color': '#000000', 'hz_line_color': '#000000', 'hz_line_type': 0, 'vt_line_type': 0, 'size': 3, 'shape': 'circle', 'draw_descendants': True, 'hz_line_width': 0, 'vt_line_width': 0}
If that is still giving you an error try instead: (which is how it is solved in CanSNPer)
from ete3 import NodeStyle NodeStyle() {'fgcolor': '#0030c1', 'bgcolor': '#FFFFFF', 'vt_line_color': '#000000', 'hz_line_color': '#000000', 'hz_line_type': 0, 'vt_line_type': 0, 'size': 3, 'shape': 'circle', 'draw_descendants': True, 'hz_line_width': 0, 'vt_line_width': 0}
Seems you have the old channel order. Bioconda changed this last year to be dependent on conda-forge. Please follow the instructions here to correct it and then re-run
conda create --name cansnper2 -y cansnper2
I fixed the channel order, but I'm getting the same result.
$ python
Python 3.8.2 | packaged by conda-forge | (default, Apr 24 2020, 08:20:52)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from ete3 import NodeStyle
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: cannot import name 'NodeStyle' from 'ete3' (/home/standage/anaconda3/envs/cansnper2/lib/python3.8/site-packages/ete3/__init__.py)
>>> import ete3
>>> ete3.NodeStyle()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: module 'ete3' has no attribute 'NodeStyle'
Hello again! I've been digging through this again, but unable to find root cause. Any luck on your end?
xref from CanSNPer1: adrlar/CanSNPer#28 were @standage mention the following issue with installing CanSNPer2.
I was able to install CanSNPer2 in a new Conda environment, and download the Ft database. But unfortunately I get the following error when I run it on an Ft sample.