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From: 范宏成 <187...@16...> - 2021-11-25 09:29:48
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Hi Pablo, Alberto and Grigory, According to your advice, I immediately deactivated the eman and successfully installed the scipion3 and xmipp according to the Installing Xmipp on Centos 7 . I have seen some new protocols in scipion3. I wanna know what the difference between highres and metaprotocol golden highres? what is the meaning of Zernike3D? I recently read this paper << DeepAlign, a 3D alignment method based on regionlaized deep learning for Cryo-EM>>. I wanna know whether the scipion version (v3.0.9 -Eugenius -3.0.17 core) with xmipp (xmippSrc-3.21.09.0) has the DeepAlign and refine consensus Tools? I didn't find yet. Thank you! Hongcheng Fan |
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From: Carlos O. S. <co...@cn...> - 2021-11-24 15:05:12
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Dear Lizelle, I am forwarding your mail to Slavica, who is the person in charge of ContinuousFlex. Kind regards, Carlos Oscar El 24/11/2021 a las 15:58, Lizelle Lubbe via scipion-users escribió: > Hi everyone, > > I would like to run HEMNMA on my particles and have done the NMA step > using an atomic model. Is there any way to visualize the trajectories > other than through VMD in Scipion? I am accessing the campus computer > with Scipion remotely and it seems like VMD installation may be an issue. > > Three modes from an input PDB show high collectivity with low scores > and I would like to now try NMA alignment with these modes. Given the > high computational cost of the protocol, is it recommended to use a > subset of particles for the analysis at present? The original stack is > of ~100k particles (discrete heterogeneity was removed by 2 rounds of > 2D classification and some 3D classifications but there is still > continuous heterogeneity). It would be great to see the full range of > variations with all particles but maybe not computationally feasible > at present? The box size at 1.06A/pix is 256 so I can maybe bin by 4 > to 64pix but windowing further will cut into my particle. > We have 256GB RAM with 24 Intel(R) Xeon(R) Silver 4214R CPU @ 2.40GHz > and 4 Quadro RTX 5000 GPUs. > > Kind regards, > Lizelle > Disclaimer - University of Cape Town This email is subject to UCT > policies and email disclaimer published on our website at > http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 > 650 9111. If this email is not related to the business of UCT, it is > sent by the sender in an individual capacity. Please report security > incidents or abuse via > https://csirt.uct.ac.za/page/report-an-incident.php. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Lizelle L. <liz...@uc...> - 2021-11-24 14:58:57
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Hi everyone, I would like to run HEMNMA on my particles and have done the NMA step using an atomic model. Is there any way to visualize the trajectories other than through VMD in Scipion? I am accessing the campus computer with Scipion remotely and it seems like VMD installation may be an issue. Three modes from an input PDB show high collectivity with low scores and I would like to now try NMA alignment with these modes. Given the high computational cost of the protocol, is it recommended to use a subset of particles for the analysis at present? The original stack is of ~100k particles (discrete heterogeneity was removed by 2 rounds of 2D classification and some 3D classifications but there is still continuous heterogeneity). It would be great to see the full range of variations with all particles but maybe not computationally feasible at present? The box size at 1.06A/pix is 256 so I can maybe bin by 4 to 64pix but windowing further will cut into my particle. We have 256GB RAM with 24 Intel(R) Xeon(R) Silver 4214R CPU @ 2.40GHz and 4 Quadro RTX 5000 GPUs. Kind regards, Lizelle Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php. |
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From: Grigory S. <sha...@gm...> - 2021-11-24 12:43:51
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Hi, looking at (base) [fanhc@localhost scipion]$ ./scipion3 installp -p scipion-em-xmipp -j 12 | tee -a install.log I'm 99% sure you have eman activated. Eman installer does a horrible thing by modifying bashrc by default so that it's always activated. You should not install scipion into eman environment Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Nov 24, 2021 at 12:40 PM Alberto Garcia Mena < alb...@cn...> wrote: > Hello 范宏成, > > Please be sure you have activate conda enviroment. > > Follow the steps described here > <https://scipion-em.github.io/docs/scipion3_instalation/docs/scipion-modes/install-from-sources.html> > : > > *sudo yum install gcc gcc-c++ openmpi-devel > export PATH=$PATH:/usr/lib64/openmpi/bin/:/usr/local/cuda/bin > conda activate > pip install --user scipion-installer > python3 -m scipioninstaller /path/where/you/want/scipion -j 4 > * > > and for the xmipp plugin, follow this steps Installing Xmipp on Centos 7 > <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009> > > Thanks > > > On 24/11/21 12:56, 范宏成 wrote: > > Hi all, > I recently intalled the scipion3 in my workstation(Cenos7) I faced the > followting problems. How to fix it? Thank you! > Hongcheng Fan > > (base) [fanhc@localhost scipion]$ ./scipion3 installp -p scipion-em-xmipp > -j 12 | tee -a install.log > Collecting scipion-em-xmipp==21.9.0 > Using cached scipion_em_xmipp-21.9.0-py3-none-any.whl > Collecting scons > Using cached SCons-4.3.0-py3-none-any.whl (4.2 MB) > Collecting plotter > Using cached plotter-1.3.19-py3-none-any.whl (11 kB) > Collecting scikit-learn==0.22.1 > Using cached scikit_learn-0.22.1-cp38-cp38-manylinux1_x86_64.whl (7.0 MB) > Collecting joblib > Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB) > Collecting peppercorn > Using cached peppercorn-0.6-py3-none-any.whl (4.8 kB) > Collecting PyWavelets > Using cached > PyWavelets-1.2.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (6.3 > MB) > Collecting scipy>=0.17.0 > Using cached > scipy-1.7.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.3 > MB) > Requirement already satisfied: numpy>=1.11.0 in > /data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages (from > scikit-learn==0.22.1->scipion-em-xmipp==21.9.0) (1.18.4) > Requirement already satisfied: setuptools in > /data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages (from > scons->scipion-em-xmipp==21.9.0) (58.0.4) > Installing collected packages: scipy, joblib, scons, scikit-learn, > PyWavelets, plotter, peppercorn, scipion-em-xmipp > Successfully installed PyWavelets-1.2.0 joblib-1.1.0 peppercorn-0.6 > plotter-1.3.19 scikit-learn-0.22.1 scipion-em-xmipp-21.9.0 scipy-1.7.2 > scons-4.3.0 > Configuring ----------------------------------------- > gcc detected > g++ found in /bin/g++ > g++ found in /bin/g++ > 'libfftw3' not found in the system > Trying to install fftw with conda > conda activate scipion3 ; conda install fftw -y -c defaults > > CommandNotFoundError: Your shell has not been properly configured to use > 'conda activate'. > To initialize your shell, run > > $ conda init <SHELL_NAME> > > Currently supported shells are: > - bash > - fish > - tcsh > - xonsh > - zsh > - powershell > > See 'conda init --help' for more information and options. > > IMPORTANT: You may need to close and restart your shell after running > 'conda init'. > > > Collecting package metadata (repodata.json): ...working... done > Solving environment: ...working... > The environment is inconsistent, please check the package plan carefully > The following packages are causing the inconsistency: > > - defaults/linux-64::libstdcxx-ng==9.3.0=hd4cf53a_17 > - defaults/linux-64::libgcc-ng==9.3.0=h5101ec6_17 > - defaults/linux-64::libffi==3.3=he6710b0_2 > - defaults/linux-64::ncurses==6.3=h7f8727e_2 > - defaults/linux-64::openssl==1.1.1l=h7f8727e_0 > - defaults/linux-64::xz==5.2.5=h7b6447c_0 > - defaults/linux-64::zlib==1.2.11=h7b6447c_3 > - defaults/linux-64::readline==8.1=h27cfd23_0 > - defaults/linux-64::tk==8.6.11=h1ccaba5_0 > - defaults/linux-64::sqlite==3.36.0=hc218d9a_0 > - defaults/linux-64::python==3.8.12=h12debd9_0 > - defaults/linux-64::certifi==2021.10.8=py38h06a4308_0 > - defaults/noarch::wheel==0.37.0=pyhd3eb1b0_1 > - defaults/linux-64::setuptools==58.0.4=py38h06a4308_0 > - defaults/linux-64::pip==21.2.4=py38h06a4308_0 > done > /bin/sh: line 1: 25730 Segmentation fault (core dumped) conda install > fftw -y -c defaults > CUDA-8.0.44 detected. > CUDA-10.2 is recommended. > Checking for compatible GCC to be used with your CUDA > No valid compiler found. Skipping CUDA compilation. > To manually set the compiler, export CXX_CUDA=/path/to/requested_compiler' > and run again 'xmipp config'. > 'mpirun' detected. > 'mpicc' detected. > 'mpicxx' detected. > Java detected at: > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64 > Matlab detected at /opt/Matlab_R2017b/bin > > Do you want to build tests [yes/NO] False > Configuration completed..... > Checking configuration ------------------------------ > Checking compiler configuration ... > Detected /bin/g++ in version 4.8.5. > Version 6.0 or higher is required. > Traceback (most recent call last): > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/data3/fanhc/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > Error at main: target > '/data3/fanhc/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > > Scipion v3.0.9 - Eugenius > Building scipion-em-xmipp ... > /data1/fanhc/miniconda3/envs/scipion3/bin/python -m pip install > scipion-em-xmipp==21.9.0 > Done (12.35 seconds) > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin > manager window) > > > Building xmippSrc-3.21.09.0 ... > Skipping command: wget -nv -c -O > /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.21.09.0.tgz > mv -v /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz.part > /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.21.09.0.tgz > All targets exist. > cd /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0 > cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp > compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null > (base) [fanhc@localhost scipion]$ ls > config install.log scipion3 software > (base) [fanhc@localhost scipion]$ gedit install.log > > (gedit:25963): GLib-GIO-CRITICAL **: 04:18:19.895: g_dbus_proxy_new_sync: > assertion 'G_IS_DBUS_CONNECTION (connection)' failed > > (gedit:25963): dconf-WARNING **: 04:18:19.912: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:19.934: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.127: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.128: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.128: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > ** (gedit:25963): WARNING **: 04:18:26.209: Set document metadata failed: > Setting attribute metadata::gedit-position not supported > > (gedit:25963): dconf-WARNING **: 04:18:26.220: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > (base) [fanhc@localhost scipion]$ > > > > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > - Alberto GM - > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Alberto G. M. <alb...@cn...> - 2021-11-24 12:39:49
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Hello 范宏成, Please be sure you have activate conda enviroment. Follow the steps described here <https://scipion-em.github.io/docs/scipion3_instalation/docs/scipion-modes/install-from-sources.html>: /sudo yum install gcc gcc-c++ openmpi-devel export PATH=$PATH:/usr/lib64/openmpi/bin/:/usr/local/cuda/bin conda activate pip install --user scipion-installer python3 -m scipioninstaller /path/where/you/want/scipion -j 4 / and for the xmipp plugin, follow this steps Installing Xmipp on Centos 7 <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009> Thanks On 24/11/21 12:56, 范宏成 wrote: > Hi all, > I recently intalled the scipion3 in my workstation(Cenos7) I faced the > followting problems. How to fix it? Thank you! > Hongcheng Fan > > (base) [fanhc@localhost scipion]$ ./scipion3 installp -p > scipion-em-xmipp -j 12 | tee -a install.log > Collecting scipion-em-xmipp==21.9.0 > Using cached scipion_em_xmipp-21.9.0-py3-none-any.whl > Collecting scons > Using cached SCons-4.3.0-py3-none-any.whl (4.2 MB) > Collecting plotter > Using cached plotter-1.3.19-py3-none-any.whl (11 kB) > Collecting scikit-learn==0.22.1 > Using cached scikit_learn-0.22.1-cp38-cp38-manylinux1_x86_64.whl > (7.0 MB) > Collecting joblib > Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB) > Collecting peppercorn > Using cached peppercorn-0.6-py3-none-any.whl (4.8 kB) > Collecting PyWavelets > Using cached > PyWavelets-1.2.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl > (6.3 MB) > Collecting scipy>=0.17.0 > Using cached > scipy-1.7.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl > (39.3 MB) > Requirement already satisfied: numpy>=1.11.0 in > /data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages > (from scikit-learn==0.22.1->scipion-em-xmipp==21.9.0) (1.18.4) > Requirement already satisfied: setuptools in > /data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages > (from scons->scipion-em-xmipp==21.9.0) (58.0.4) > Installing collected packages: scipy, joblib, scons, scikit-learn, > PyWavelets, plotter, peppercorn, scipion-em-xmipp > Successfully installed PyWavelets-1.2.0 joblib-1.1.0 peppercorn-0.6 > plotter-1.3.19 scikit-learn-0.22.1 scipion-em-xmipp-21.9.0 scipy-1.7.2 > scons-4.3.0 > Configuring ----------------------------------------- > gcc detected > g++ found in /bin/g++ > g++ found in /bin/g++ > 'libfftw3' not found in the system > Trying to install fftw with conda > conda activate scipion3 ; conda install fftw -y -c defaults > > CommandNotFoundError: Your shell has not been properly configured to > use 'conda activate'. > To initialize your shell, run > > $ conda init <SHELL_NAME> > > Currently supported shells are: > - bash > - fish > - tcsh > - xonsh > - zsh > - powershell > > See 'conda init --help' for more information and options. > > IMPORTANT: You may need to close and restart your shell after running > 'conda init'. > > > Collecting package metadata (repodata.json): ...working... done > Solving environment: ...working... > The environment is inconsistent, please check the package plan carefully > The following packages are causing the inconsistency: > > - defaults/linux-64::libstdcxx-ng==9.3.0=hd4cf53a_17 > - defaults/linux-64::libgcc-ng==9.3.0=h5101ec6_17 > - defaults/linux-64::libffi==3.3=he6710b0_2 > - defaults/linux-64::ncurses==6.3=h7f8727e_2 > - defaults/linux-64::openssl==1.1.1l=h7f8727e_0 > - defaults/linux-64::xz==5.2.5=h7b6447c_0 > - defaults/linux-64::zlib==1.2.11=h7b6447c_3 > - defaults/linux-64::readline==8.1=h27cfd23_0 > - defaults/linux-64::tk==8.6.11=h1ccaba5_0 > - defaults/linux-64::sqlite==3.36.0=hc218d9a_0 > - defaults/linux-64::python==3.8.12=h12debd9_0 > - defaults/linux-64::certifi==2021.10.8=py38h06a4308_0 > - defaults/noarch::wheel==0.37.0=pyhd3eb1b0_1 > - defaults/linux-64::setuptools==58.0.4=py38h06a4308_0 > - defaults/linux-64::pip==21.2.4=py38h06a4308_0 > done > /bin/sh: line 1: 25730 Segmentation fault (core dumped) conda > install fftw -y -c defaults > CUDA-8.0.44 detected. > CUDA-10.2 is recommended. > Checking for compatible GCC to be used with your CUDA > No valid compiler found. Skipping CUDA compilation. > To manually set the compiler, export > CXX_CUDA=/path/to/requested_compiler' and run again 'xmipp config'. > 'mpirun' detected. > 'mpicc' detected. > 'mpicxx' detected. > Java detected at: > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64 > Matlab detected at /opt/Matlab_R2017b/bin > > Do you want to build tests [yes/NO] False > Configuration completed..... > Checking configuration ------------------------------ > Checking compiler configuration ... > Detected /bin/g++ in version 4.8.5. > Version 6.0 or higher is required. > Traceback (most recent call last): > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/data3/fanhc/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > Error at main: target > '/data3/fanhc/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > > Scipion v3.0.9 - Eugenius > Building scipion-em-xmipp ... > /data1/fanhc/miniconda3/envs/scipion3/bin/python -m pip install > scipion-em-xmipp==21.9.0 > Done (12.35 seconds) > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin > manager window) > > > Building xmippSrc-3.21.09.0 ... > Skipping command: wget -nv -c -O > /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.21.09.0.tgz > mv -v /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz.part > /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.21.09.0.tgz > All targets exist. > cd /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0 > cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp > compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null > (base) [fanhc@localhost scipion]$ ls > config install.log scipion3 software > (base) [fanhc@localhost scipion]$ gedit install.log > > (gedit:25963): GLib-GIO-CRITICAL **: 04:18:19.895: > g_dbus_proxy_new_sync: assertion 'G_IS_DBUS_CONNECTION (connection)' > failed > > (gedit:25963): dconf-WARNING **: 04:18:19.912: failed to commit > changes to dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:19.934: failed to commit > changes to dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.127: failed to commit > changes to dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.128: failed to commit > changes to dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.128: failed to commit > changes to dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > ** (gedit:25963): WARNING **: 04:18:26.209: Set document metadata > failed: Setting attribute metadata::gedit-position not supported > > (gedit:25963): dconf-WARNING **: 04:18:26.220: failed to commit > changes to dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > (base) [fanhc@localhost scipion]$ > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
|
From: Pablo C. <pc...@cn...> - 2021-11-24 12:37:46
|
Try to Install libfftw3 on the system using yum? On 24/11/21 12:56, 范宏成 wrote: > 'libfftw3' not found in the system > Trying to install fftw with conda -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: 范宏成 <187...@16...> - 2021-11-24 11:56:52
|
Hi all,
I recently intalled the scipion3 in my workstation(Cenos7) I faced the followting problems. How to fix it? Thank you!
Hongcheng Fan
(base) [fanhc@localhost scipion]$ ./scipion3 installp -p scipion-em-xmipp -j 12 | tee -a install.log
Collecting scipion-em-xmipp==21.9.0
Using cached scipion_em_xmipp-21.9.0-py3-none-any.whl
Collecting scons
Using cached SCons-4.3.0-py3-none-any.whl (4.2 MB)
Collecting plotter
Using cached plotter-1.3.19-py3-none-any.whl (11 kB)
Collecting scikit-learn==0.22.1
Using cached scikit_learn-0.22.1-cp38-cp38-manylinux1_x86_64.whl (7.0 MB)
Collecting joblib
Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB)
Collecting peppercorn
Using cached peppercorn-0.6-py3-none-any.whl (4.8 kB)
Collecting PyWavelets
Using cached PyWavelets-1.2.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (6.3 MB)
Collecting scipy>=0.17.0
Using cached scipy-1.7.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.3 MB)
Requirement already satisfied: numpy>=1.11.0 in /data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==21.9.0) (1.18.4)
Requirement already satisfied: setuptools in /data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages (from scons->scipion-em-xmipp==21.9.0) (58.0.4)
Installing collected packages: scipy, joblib, scons, scikit-learn, PyWavelets, plotter, peppercorn, scipion-em-xmipp
Successfully installed PyWavelets-1.2.0 joblib-1.1.0 peppercorn-0.6 plotter-1.3.19 scikit-learn-0.22.1 scipion-em-xmipp-21.9.0 scipy-1.7.2 scons-4.3.0
Configuring -----------------------------------------
gcc detected
g++ found in /bin/g++
g++ found in /bin/g++
'libfftw3' not found in the system
Trying to install fftw with conda
conda activate scipion3 ; conda install fftw -y -c defaults
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working...
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- defaults/linux-64::libstdcxx-ng==9.3.0=hd4cf53a_17
- defaults/linux-64::libgcc-ng==9.3.0=h5101ec6_17
- defaults/linux-64::libffi==3.3=he6710b0_2
- defaults/linux-64::ncurses==6.3=h7f8727e_2
- defaults/linux-64::openssl==1.1.1l=h7f8727e_0
- defaults/linux-64::xz==5.2.5=h7b6447c_0
- defaults/linux-64::zlib==1.2.11=h7b6447c_3
- defaults/linux-64::readline==8.1=h27cfd23_0
- defaults/linux-64::tk==8.6.11=h1ccaba5_0
- defaults/linux-64::sqlite==3.36.0=hc218d9a_0
- defaults/linux-64::python==3.8.12=h12debd9_0
- defaults/linux-64::certifi==2021.10.8=py38h06a4308_0
- defaults/noarch::wheel==0.37.0=pyhd3eb1b0_1
- defaults/linux-64::setuptools==58.0.4=py38h06a4308_0
- defaults/linux-64::pip==21.2.4=py38h06a4308_0
done
/bin/sh: line 1: 25730 Segmentation fault (core dumped) conda install fftw -y -c defaults
CUDA-8.0.44 detected.
CUDA-10.2 is recommended.
Checking for compatible GCC to be used with your CUDA
No valid compiler found. Skipping CUDA compilation.
To manually set the compiler, export CXX_CUDA=/path/to/requested_compiler' and run again 'xmipp config'.
'mpirun' detected.
'mpicc' detected.
'mpicxx' detected.
Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64
Matlab detected at /opt/Matlab_R2017b/bin
Do you want to build tests [yes/NO] False
Configuration completed.....
Checking configuration ------------------------------
Checking compiler configuration ...
Detected /bin/g++ in version 4.8.5.
Version 6.0 or higher is required.
Traceback (most recent call last):
File "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module>
main()
File "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main
installPluginMethods()
File "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
command.execute()
File "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/data3/fanhc/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=12 && ln -srfn build /data3/fanhc/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Error at main: target '/data3/fanhc/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=12 && ln -srfn build /data3/fanhc/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Scipion v3.0.9 - Eugenius
Building scipion-em-xmipp ...
/data1/fanhc/miniconda3/envs/scipion3/bin/python -m pip install scipion-em-xmipp==21.9.0
Done (12.35 seconds)
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
Building xmippSrc-3.21.09.0 ...
Skipping command: wget -nv -c -O /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.21.09.0.tgz
mv -v /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz.part /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz
All targets exist.
Skipping command: tar -xf xmippSrc-v3.21.09.0.tgz
All targets exist.
cd /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0
cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=12 && ln -srfn build /data3/fanhc/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null
(base) [fanhc@localhost scipion]$ ls
config install.log scipion3 software
(base) [fanhc@localhost scipion]$ gedit install.log
(gedit:25963): GLib-GIO-CRITICAL **: 04:18:19.895: g_dbus_proxy_new_sync: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gedit:25963): dconf-WARNING **: 04:18:19.912: failed to commit changes to dconf: Error spawning command line “dbus-launch --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax --close-stderr”: Child process exited with code 1
(gedit:25963): dconf-WARNING **: 04:18:19.934: failed to commit changes to dconf: Error spawning command line “dbus-launch --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax --close-stderr”: Child process exited with code 1
(gedit:25963): dconf-WARNING **: 04:18:20.127: failed to commit changes to dconf: Error spawning command line “dbus-launch --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax --close-stderr”: Child process exited with code 1
(gedit:25963): dconf-WARNING **: 04:18:20.128: failed to commit changes to dconf: Error spawning command line “dbus-launch --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax --close-stderr”: Child process exited with code 1
(gedit:25963): dconf-WARNING **: 04:18:20.128: failed to commit changes to dconf: Error spawning command line “dbus-launch --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax --close-stderr”: Child process exited with code 1
** (gedit:25963): WARNING **: 04:18:26.209: Set document metadata failed: Setting attribute metadata::gedit-position not supported
(gedit:25963): dconf-WARNING **: 04:18:26.220: failed to commit changes to dconf: Error spawning command line “dbus-launch --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax --close-stderr”: Child process exited with code 1
(base) [fanhc@localhost scipion]$
|
|
From: Pablo C. <pc...@cn...> - 2021-11-24 11:22:08
|
Great! Thanks for confirming it.
On 24/11/21 9:27, #CHEW BING LIANG ALVIN# wrote:
> Dear Pablo,
>
> Thank you! Changing the scipion3 launcher works!
>
>
> os.environ["PATH"] =
> ":".join(["/home/dlsw1/anaconda/envs/scipion3/bin",
> os.environ.get("PATH", "")])
>
>
> BestRegards
>
> Alvin CHEW | Ph.D. Student |Lee Kong Chian School of Medicine | NTU
> Institute for HealthTechnologies (HealthTech NTU), Interdisciplinary
> Graduate Programme| Nanyang Technological University | 59 Nanyang
> Drive, Experimental Medicine Building, 03-07-01, Singapore 636921Tel:
> (65) 6592-3990 GMT+8h| Email: chew0357@e.ntu.edu.sg | Web:
> http://www.lkcmedicine.ntu.edu.sg <http://www.lkcmedicine.ntu.edu.sg/>
>
> /"(You) who (have) a why to live can bear almost any how.//"/
> ~Friedrich Nietzsche
> <http://www.brainyquote.com/quotes/quotes/f/friedrichn103819.html>~
>
> CONFIDENTIALITY: This email is intended solely for the person(s) named
> and may be confidential and/or privileged. If you are not the intended
> recipient, please delete it, notify us and do not copy, use, or
> disclose its contents.
>
>
> ------------------------------------------------------------------------
> *From:* Pablo Conesa <pc...@cn...>
> *Sent:* Wednesday, October 27, 2021 4:51 PM
> *To:* sci...@li...
> <sci...@li...>
> *Subject:* Re: [scipion-users] [Troubleshooting request] Error opening
> scipion3 after topaz installation
>
> I think the problem resides in the last image.
>
>
> You are adding topaz's python to the PATH making it the default python
> and that one is taking priority over other pythons, even when
> activating environments
>
>
> Can you make a quick test?
>
>
> 1.- Comment the line in your bash.rc where you are addig topaz to the
> PATH variable.
>
> 2.- Close the terminal and open it again (or source your bash.rc)
>
> 3.- Try to run Scipion3
>
>
> Alternatively, you might want to modify scipion3 launcher adding a
> line to prioritize scipion python?
>
>
> os.environ["PATH"] =
> ":".join(["/home/dlsw1/anaconda/envs/scipion3/bin",
> os.environ.get("PATH", "")])
>
>
> Haven't tried it.
>
>
> On 27/10/21 5:00, #CHEW BING LIANG ALVIN# wrote:
>> Dear Scipion community,
>>
>> I had no issues using scipion3 until I have installed topaz under the
>> installation instructions listed in cryosparc
>> https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz
>> <https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz>
>> I have tried reading through the troubleshooting guide but could not
>> seem to find a solution to my problem here.
>> I have attached various screenshots that show the path pointed out by
>> "scipion3" command points to topaz, but this is not the case in my
>> bashrc setting. Screenshots *_1 and *_2 are the list of documents in
>> the Programme and anaconda env.
>> I could not seem to find the scipion.conf file as well, I am unsure
>> if setting the scipion.conf is the fix I need in my case or simply
>> reinstall scipion3 by following the installation guide again?
>>
>> Thank you and hope to receive any useful advice on how to proceed.
>>
>> BestRegards
>>
>> Alvin CHEW | Ph.D. Student |Nanyang Technological University
>> |<http://www.lkcmedicine.ntu.edu.sg/>
>>
>> /"(You) who (have) a why to live can bear almost any how.//"/
>> ~Friedrich Nietzsche
>> <http://www.brainyquote.com/quotes/quotes/f/friedrichn103819.html>~
>>
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li... <mailto:sci...@li...>
>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: #CHEW B. L. A. <CHEW0357@e.ntu.edu.sg> - 2021-11-24 09:02:25
|
Dear Pablo,
Thank you! Changing the scipion3 launcher works!
os.environ["PATH"] = ":".join(["/home/dlsw1/anaconda/envs/scipion3/bin", os.environ.get("PATH", "")])
Best Regards
Alvin CHEW | Ph.D. Student | Lee Kong Chian School of Medicine | NTU Institute for Health Technologies (HealthTech NTU), Interdisciplinary Graduate Programme | Nanyang Technological University | 59 Nanyang Drive, Experimental Medicine Building, 03-07-01, Singapore 636921Tel: (65) 6592-3990 GMT+8h| Email: chew0357@e.ntu.edu.sg | Web: http://www.lkcmedicine.ntu.edu.sg<http://www.lkcmedicine.ntu.edu.sg/>
"(You) who (have) a why to live can bear almost any how."
~Friedrich Nietzsche<http://www.brainyquote.com/quotes/quotes/f/friedrichn103819.html>~
CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents.
________________________________
From: Pablo Conesa <pc...@cn...>
Sent: Wednesday, October 27, 2021 4:51 PM
To: sci...@li... <sci...@li...>
Subject: Re: [scipion-users] [Troubleshooting request] Error opening scipion3 after topaz installation
I think the problem resides in the last image.
You are adding topaz's python to the PATH making it the default python and that one is taking priority over other pythons, even when activating environments
Can you make a quick test?
1.- Comment the line in your bash.rc where you are addig topaz to the PATH variable.
2.- Close the terminal and open it again (or source your bash.rc)
3.- Try to run Scipion3
Alternatively, you might want to modify scipion3 launcher adding a line to prioritize scipion python?
os.environ["PATH"] = ":".join(["/home/dlsw1/anaconda/envs/scipion3/bin", os.environ.get("PATH", "")])
Haven't tried it.
On 27/10/21 5:00, #CHEW BING LIANG ALVIN# wrote:
Dear Scipion community,
I had no issues using scipion3 until I have installed topaz under the installation instructions listed in cryosparc https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz
I have tried reading through the troubleshooting guide but could not seem to find a solution to my problem here.
I have attached various screenshots that show the path pointed out by "scipion3" command points to topaz, but this is not the case in my bashrc setting. Screenshots *_1 and *_2 are the list of documents in the Programme and anaconda env.
I could not seem to find the scipion.conf file as well, I am unsure if setting the scipion.conf is the fix I need in my case or simply reinstall scipion3 by following the installation guide again?
Thank you and hope to receive any useful advice on how to proceed.
Best Regards
Alvin CHEW | Ph.D. Student | Nanyang Technological University |<http://www.lkcmedicine.ntu.edu.sg/>
"(You) who (have) a why to live can bear almost any how."
~Friedrich Nietzsche<http://www.brainyquote.com/quotes/quotes/f/friedrichn103819.html>~
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team
|
|
From: Lizelle L. <liz...@uc...> - 2021-11-23 17:55:19
|
Okay, thanks Grigory! ________________________________ From: Grigory Sharov <sha...@gm...> Sent: Tuesday, 23 November 2021 18:41 To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] Import particles to scipion from csparc2star or relion3.1 CAUTION: This email originated outside the UCT network. Do not click any links or open attachments unless you know and trust the source. Hi, For Relion3 RELION_HOME folder should be called relion-3.1.x, where x is 0/1/2/3. There's no other way for the plugin to recognize the version. You can make a symlink with such a name pointing to any folder. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Tue, Nov 23, 2021 at 4:14 PM Lizelle Lubbe via scipion-users <sci...@li...<mailto:sci...@li...>> wrote: Hi, I am trying to import two particle stacks to scipion but get the message: error reading the following images: /home/lbbliz002/ptcls_for_HEMNMA/particles.star The one particle stack is a star file from RELION version: 3.1.0-commit-1349c5 while the other was exported from cryoSPARC v3.2, the .cs file converted using csparc2star.py, and then all particles given the extension .mrcs in the star file using sed. Both stacks give the same error message. My scipion.config file contains the following: [PLUGINS] BSOFT_HOME = %(EM_ROOT)s/bsoft-2.0.7 CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.1 CRYOASSESS_ENV_ACTIVATION = conda activate cryoassess-0.2.0 CRYOASSESS_MODEL_2D = %(EM_ROOT)s/cryoassess-models/2dassess_062119.h5 CRYOASSESS_MODEL_MIC = %(EM_ROOT)s/cryoassess-models/micassess_051419.h5 EM_ROOT = software/em FSC3D_ACTIVATION_CMD = conda activate 3DFSC FSC3D_HOME = %(EM_ROOT)s/fsc3D-3.0 MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 RESMAP = ResMap-1.95-cuda-Centos7x64 RESMAP_GPU_LIB = ResMap_krnl-cuda-V8.0.61-sm60_gpu.so<http://ResMap_krnl-cuda-V8.0.61-sm60_gpu.so> RESMAP_HOME = %(EM_ROOT)s/resmap-1.95 XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src XMIPP_HOME = %(EM_ROOT)s/xmipp RELION_HOME = /opt/relion Relion3.1 is called by RELION_HOME. Any idea what I am doing wrong and how the particles can be imported? Regards Lizelle Lubbe, PhD Postdoctoral Research Assistant GCRF_START project Division of Chemical and Systems Biology Department of Integrative Biomedical Sciences Faculty of Health Sciences University of Cape Town South Africa Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer<http://www.uct.ac.za/main/email-disclaimer> or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php<https://csirt.uct.ac.za/page/report-an-incident.php>. _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://lists.sourceforge.net/lists/listinfo/scipion-users> Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php. |
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From: Grigory S. <sha...@gm...> - 2021-11-23 16:41:50
|
Hi, For Relion3 RELION_HOME folder should be called relion-3.1.x, where x is 0/1/2/3. There's no other way for the plugin to recognize the version. You can make a symlink with such a name pointing to any folder. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Tue, Nov 23, 2021 at 4:14 PM Lizelle Lubbe via scipion-users < sci...@li...> wrote: > Hi, > > I am trying to import two particle stacks to scipion but get the message: > error reading the following images: > /home/lbbliz002/ptcls_for_HEMNMA/particles.star > The one particle stack is a star file from RELION version: > 3.1.0-commit-1349c5 while the other was exported from cryoSPARC v3.2, the > .cs file converted using csparc2star.py, and then all particles given the > extension .mrcs in the star file using sed. Both stacks give the same > error message. > > My scipion.config file contains the following: > > [PLUGINS] > BSOFT_HOME = %(EM_ROOT)s/bsoft-2.0.7 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.1 > CRYOASSESS_ENV_ACTIVATION = conda activate cryoassess-0.2.0 > CRYOASSESS_MODEL_2D = %(EM_ROOT)s/cryoassess-models/2dassess_062119.h5 > CRYOASSESS_MODEL_MIC = %(EM_ROOT)s/cryoassess-models/micassess_051419.h5 > EM_ROOT = software/em > FSC3D_ACTIVATION_CMD = conda activate 3DFSC > FSC3D_HOME = %(EM_ROOT)s/fsc3D-3.0 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > RESMAP = ResMap-1.95-cuda-Centos7x64 > RESMAP_GPU_LIB = ResMap_krnl-cuda-V8.0.61-sm60_gpu.so > RESMAP_HOME = %(EM_ROOT)s/resmap-1.95 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > RELION_HOME = /opt/relion > > Relion3.1 is called by RELION_HOME. > Any idea what I am doing wrong and how the particles can be imported? > > Regards > > Lizelle Lubbe, PhD > > Postdoctoral Research Assistant > GCRF_START project > Division of Chemical and Systems Biology > Department of Integrative Biomedical Sciences > Faculty of Health Sciences > University of Cape Town > South Africa > Disclaimer - University of Cape Town This email is subject to UCT policies > and email disclaimer published on our website at > http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 > 9111. If this email is not related to the business of UCT, it is sent by > the sender in an individual capacity. Please report security incidents or > abuse via https://csirt.uct.ac.za/page/report-an-incident.php. > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Lizelle L. <liz...@uc...> - 2021-11-23 16:13:49
|
Hi, I am trying to import two particle stacks to scipion but get the message: error reading the following images: /home/lbbliz002/ptcls_for_HEMNMA/particles.star The one particle stack is a star file from RELION version: 3.1.0-commit-1349c5 while the other was exported from cryoSPARC v3.2, the .cs file converted using csparc2star.py, and then all particles given the extension .mrcs in the star file using sed. Both stacks give the same error message. My scipion.config file contains the following: [PLUGINS] BSOFT_HOME = %(EM_ROOT)s/bsoft-2.0.7 CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.1 CRYOASSESS_ENV_ACTIVATION = conda activate cryoassess-0.2.0 CRYOASSESS_MODEL_2D = %(EM_ROOT)s/cryoassess-models/2dassess_062119.h5 CRYOASSESS_MODEL_MIC = %(EM_ROOT)s/cryoassess-models/micassess_051419.h5 EM_ROOT = software/em FSC3D_ACTIVATION_CMD = conda activate 3DFSC FSC3D_HOME = %(EM_ROOT)s/fsc3D-3.0 MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 RESMAP = ResMap-1.95-cuda-Centos7x64 RESMAP_GPU_LIB = ResMap_krnl-cuda-V8.0.61-sm60_gpu.so RESMAP_HOME = %(EM_ROOT)s/resmap-1.95 XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src XMIPP_HOME = %(EM_ROOT)s/xmipp RELION_HOME = /opt/relion Relion3.1 is called by RELION_HOME. Any idea what I am doing wrong and how the particles can be imported? Regards Lizelle Lubbe, PhD Postdoctoral Research Assistant GCRF_START project Division of Chemical and Systems Biology Department of Integrative Biomedical Sciences Faculty of Health Sciences University of Cape Town South Africa Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php. |
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From: Grigory S. <sha...@gm...> - 2021-11-22 15:35:46
|
Dear Roman, this means you Scipion core is not up to date, try running: scipion update Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Nov 22, 2021 at 3:28 PM Kouril Roman <rom...@up...> wrote: > Dear colleagues, > > > > I have problem to run “Relion – 2D classification” under Scipion3. The > process fails with this error: “Envron” object has no attribute > “setPrepend”. > > > > Can anyone help me to solve this problem? > > > > Thank you for advice. > > > > With kind regards > > > > Roman Kouril > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Kouril R. <rom...@up...> - 2021-11-22 14:40:23
|
Dear colleagues, I have problem to run "Relion - 2D classification" under Scipion3. The process fails with this error: "Envron" object has no attribute "setPrepend". Can anyone help me to solve this problem? Thank you for advice. With kind regards Roman Kouril |
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From: Alberto G. M. <alb...@cn...> - 2021-11-19 10:59:13
|
Hi Lynn, At this moment (on devel branch) the most of the test pass, included those what you refer. Just as a reminder; failure of a test in xmipp does not imply that Xmipp is failing. On 10/11/21 12:36, Pablo Conesa wrote: > > Hi Lynn! > > Please do not worry about that error. The test is expecting a certain > CTF values and you are not getting them. Theses values may vary with > newer versions of the ctf estimation binaries (ccffind, gctf, ...and > so on) and the test might bot be updated. > > "AssertionError: 24140.0898 != 24025.673242 within 100 delta > (114.4165580000008 difference)" > > Means that we are expecting in the test a defocus value of > 24025.673242 +- 100 and you are getting 24140.0898. > > To me is a valid value. > > Actually, this test, like many create a project, in this case > "TestCtfConsensus". If you open the project I'd say boxes are green > and all worked fine, only the test (extrict) does not like the output. > > You should be able to ope the project with: > > scipion3 project TestCtfConsensus > > > > > On 10/11/21 12:06, Lynn Radamaker wrote: >> Dear Scipion community, >> >> the first of these errors was solved by expanding cistem in the >> plugin manager and installing Ctffind additionally. >> >> So far, I have not made any progress with the second error. When I >> open the workflow for this test project (TestXmippWorkflow) in >> Scipion, the last step is "extract coordinates applying shifts" which >> finishes successfully. Any help would be greatly appreciated. >> >> Kind regards, >> >> Lynn Radamaker >> >> >> >> On Thursday, November 04, 2021 15:33 CET, "Lynn Radamaker" >> <lyn...@un...> wrote: >>> Dear Scipion community, >>> >>> I'm having some problems with Xmipp. It installed without errors, >>> but it gives a warning that it cannot find the image library. When I >>> run this test: >>> >>> scipion3 tests >>> pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus >>> >>> Then it gives me the following error message: >>> >>> [ FAILED ] TestCtfConsensus.test1 >>> >>> Traceback (most recent call last): >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >>> line 60, in testPartExecutor >>> yield >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >>> line 676, in run >>> self._callTestMethod(testMethod) >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >>> line 633, in _callTestMethod >>> method() >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", >>> line 186, in test1 >>> self.checkCTFs(protCTFcons3, >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", >>> line 71, in checkCTFs >>> self.assertAlmostEqual(avgCTF['defocusU'], >>> firstCTF.getDefocusU(), delta=100, >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >>> line 966, in assertAlmostEqual >>> raise self.failureException(msg) >>> AssertionError: 24140.0898 != 24025.673242 within 100 delta >>> (114.4165580000008 difference) : DefocusU doesn't match when defocus >>> averaging. >>> >>> Also, the similar test: >>> >>> scipion3 tests pwem.tests.workflows.test_workflow_xmipp >>> >>> Gives the error message: >>> >>> [ FAILED ] TestXmippWorkflow.testXmippWorkflow >>> >>> Traceback (most recent call last): >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >>> line 60, in testPartExecutor >>> yield >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >>> line 676, in run >>> self._callTestMethod(testMethod) >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >>> line 633, in _callTestMethod >>> method() >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py", >>> line 198, in testXmippWorkflow >>> self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(), >>> File >>> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >>> line 943, in assertAlmostEqual >>> diff = abs(first - second) >>> TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple' >>> >>> >>> >>> All the other tests (basic and medium) that I ran completed without >>> problems. I'm hoping that you can give me some advice on how to fix >>> these error and get Xmipp running properly. >>> >>> Kind regards, >>> >>> Lynn Radamaker >>> >>> >>> >>> >> >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
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From: Pablo C. <pc...@cn...> - 2021-11-10 11:36:55
|
Hi Lynn! Please do not worry about that error. The test is expecting a certain CTF values and you are not getting them. Theses values may vary with newer versions of the ctf estimation binaries (ccffind, gctf, ...and so on) and the test might bot be updated. "AssertionError: 24140.0898 != 24025.673242 within 100 delta (114.4165580000008 difference)" Means that we are expecting in the test a defocus value of 24025.673242 +- 100 and you are getting 24140.0898. To me is a valid value. Actually, this test, like many create a project, in this case "TestCtfConsensus". If you open the project I'd say boxes are green and all worked fine, only the test (extrict) does not like the output. You should be able to ope the project with: scipion3 project TestCtfConsensus On 10/11/21 12:06, Lynn Radamaker wrote: > Dear Scipion community, > > the first of these errors was solved by expanding cistem in the plugin > manager and installing Ctffind additionally. > > So far, I have not made any progress with the second error. When I > open the workflow for this test project (TestXmippWorkflow) in > Scipion, the last step is "extract coordinates applying shifts" which > finishes successfully. Any help would be greatly appreciated. > > Kind regards, > > Lynn Radamaker > > > > On Thursday, November 04, 2021 15:33 CET, "Lynn Radamaker" > <lyn...@un...> wrote: >> Dear Scipion community, >> >> I'm having some problems with Xmipp. It installed without errors, but >> it gives a warning that it cannot find the image library. When I run >> this test: >> >> scipion3 tests >> pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus >> >> Then it gives me the following error message: >> >> [ FAILED ] TestCtfConsensus.test1 >> >> Traceback (most recent call last): >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 60, in testPartExecutor >> yield >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 676, in run >> self._callTestMethod(testMethod) >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 633, in _callTestMethod >> method() >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", >> line 186, in test1 >> self.checkCTFs(protCTFcons3, >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", >> line 71, in checkCTFs >> self.assertAlmostEqual(avgCTF['defocusU'], >> firstCTF.getDefocusU(), delta=100, >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 966, in assertAlmostEqual >> raise self.failureException(msg) >> AssertionError: 24140.0898 != 24025.673242 within 100 delta >> (114.4165580000008 difference) : DefocusU doesn't match when defocus >> averaging. >> >> Also, the similar test: >> >> scipion3 tests pwem.tests.workflows.test_workflow_xmipp >> >> Gives the error message: >> >> [ FAILED ] TestXmippWorkflow.testXmippWorkflow >> >> Traceback (most recent call last): >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 60, in testPartExecutor >> yield >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 676, in run >> self._callTestMethod(testMethod) >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 633, in _callTestMethod >> method() >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py", >> line 198, in testXmippWorkflow >> self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(), >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 943, in assertAlmostEqual >> diff = abs(first - second) >> TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple' >> >> >> >> All the other tests (basic and medium) that I ran completed without >> problems. I'm hoping that you can give me some advice on how to fix >> these error and get Xmipp running properly. >> >> Kind regards, >> >> Lynn Radamaker >> >> >> >> > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Lynn R. <lyn...@un...> - 2021-11-10 11:06:31
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Dear Scipion community, the first of these errors was solved by expanding cistem in the plugin manager and installing Ctffind additionally. So far, I have not made any progress with the second error. When I open the workflow for this test project (TestXmippWorkflow) in Scipion, the last step is "extract coordinates applying shifts" which finishes successfully. Any help would be greatly appreciated. Kind regards, Lynn Radamaker On Thursday, November 04, 2021 15:33 CET, "Lynn Radamaker" <lyn...@un...> wrote: Dear Scipion community, I'm having some problems with Xmipp. It installed without errors, but it gives a warning that it cannot find the image library. When I run this test: scipion3 tests pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus Then it gives me the following error message: [ FAILED ] TestCtfConsensus.test1 Traceback (most recent call last): File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor yield File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run self._callTestMethod(testMethod) File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod method() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", line 186, in test1 self.checkCTFs(protCTFcons3, File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", line 71, in checkCTFs self.assertAlmostEqual(avgCTF['defocusU'], firstCTF.getDefocusU(), delta=100, File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 966, in assertAlmostEqual raise self.failureException(msg) AssertionError: 24140.0898 != 24025.673242 within 100 delta (114.4165580000008 difference) : DefocusU doesn't match when defocus averaging. Also, the similar test: scipion3 tests pwem.tests.workflows.test_workflow_xmipp Gives the error message: [ FAILED ] TestXmippWorkflow.testXmippWorkflow Traceback (most recent call last): File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor yield File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run self._callTestMethod(testMethod) File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod method() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py", line 198, in testXmippWorkflow self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(), File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 943, in assertAlmostEqual diff = abs(first - second) TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple' All the other tests (basic and medium) that I ran completed without problems. I'm hoping that you can give me some advice on how to fix these error and get Xmipp running properly. Kind regards, Lynn Radamaker |
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From: Alberto G. M. <alb...@cn...> - 2021-11-05 13:40:42
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Hello Lynn, Thanks for the information. We are working on it. In the devel brach sometimes we have some test fails and as fast as we can we fix it. Thanks On 5/11/21 8:37, Carlos Oscar Sorzano wrote: > > Dear Lynn, > > this error is not familiar to me. Alberto will help you to find what > is happening. > > Kind regards, Carlos Oscar > > El 04/11/2021 a las 15:33, Lynn Radamaker escribió: >> Dear Scipion community, >> >> I'm having some problems with Xmipp. It installed without errors, but >> it gives a warning that it cannot find the image library. When I run >> this test: >> >> scipion3 tests >> pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus >> >> Then it gives me the following error message: >> >> [ FAILED ] TestCtfConsensus.test1 >> >> Traceback (most recent call last): >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 60, in testPartExecutor >> yield >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 676, in run >> self._callTestMethod(testMethod) >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 633, in _callTestMethod >> method() >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", >> line 186, in test1 >> self.checkCTFs(protCTFcons3, >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", >> line 71, in checkCTFs >> self.assertAlmostEqual(avgCTF['defocusU'], >> firstCTF.getDefocusU(), delta=100, >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 966, in assertAlmostEqual >> raise self.failureException(msg) >> AssertionError: 24140.0898 != 24025.673242 within 100 delta >> (114.4165580000008 difference) : DefocusU doesn't match when defocus >> averaging. >> >> Also, the similar test: >> >> scipion3 tests pwem.tests.workflows.test_workflow_xmipp >> >> Gives the error message: >> >> [ FAILED ] TestXmippWorkflow.testXmippWorkflow >> >> Traceback (most recent call last): >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 60, in testPartExecutor >> yield >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 676, in run >> self._callTestMethod(testMethod) >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 633, in _callTestMethod >> method() >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py", >> line 198, in testXmippWorkflow >> self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(), >> File >> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", >> line 943, in assertAlmostEqual >> diff = abs(first - second) >> TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple' >> >> >> >> All the other tests (basic and medium) that I ran completed without >> problems. I'm hoping that you can give me some advice on how to fix >> these error and get Xmipp running properly. >> >> Kind regards, >> >> Lynn Radamaker >> >> >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
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From: Carlos O. S. <co...@cn...> - 2021-11-05 07:37:51
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Dear Lynn, this error is not familiar to me. Alberto will help you to find what is happening. Kind regards, Carlos Oscar El 04/11/2021 a las 15:33, Lynn Radamaker escribió: > Dear Scipion community, > > I'm having some problems with Xmipp. It installed without errors, but > it gives a warning that it cannot find the image library. When I run > this test: > > scipion3 tests > pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus > > Then it gives me the following error message: > > [ FAILED ] TestCtfConsensus.test1 > > Traceback (most recent call last): > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 60, in testPartExecutor > yield > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 676, in run > self._callTestMethod(testMethod) > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 633, in _callTestMethod > method() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", > line 186, in test1 > self.checkCTFs(protCTFcons3, > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", > line 71, in checkCTFs > self.assertAlmostEqual(avgCTF['defocusU'], firstCTF.getDefocusU(), > delta=100, > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 966, in assertAlmostEqual > raise self.failureException(msg) > AssertionError: 24140.0898 != 24025.673242 within 100 delta > (114.4165580000008 difference) : DefocusU doesn't match when defocus > averaging. > > Also, the similar test: > > scipion3 tests pwem.tests.workflows.test_workflow_xmipp > > Gives the error message: > > [ FAILED ] TestXmippWorkflow.testXmippWorkflow > > Traceback (most recent call last): > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 60, in testPartExecutor > yield > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 676, in run > self._callTestMethod(testMethod) > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 633, in _callTestMethod > method() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py", > line 198, in testXmippWorkflow > self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(), > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 943, in assertAlmostEqual > diff = abs(first - second) > TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple' > > > > All the other tests (basic and medium) that I ran completed without > problems. I'm hoping that you can give me some advice on how to fix > these error and get Xmipp running properly. > > Kind regards, > > Lynn Radamaker > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2021-11-04 20:27:34
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Or you are pointing to chimera 1.13. What gives you "scipion3 config -p chimera" On 4/11/21 20:05, Grigory Sharov wrote: > Dear Lynn, > > it appears you do not > have /usr/local/bin/scipion/software/em/chimerax-1.2.5/bin/ChimeraX - > main binary file, which means chimerax installation did not work. > > Have you tried removing /usr/local/bin/scipion/software/em/chimerax* > and installing again? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Nov 4, 2021 at 3:57 PM Lynn Radamaker > <lyn...@un... <mailto:lyn...@un...>> wrote: > > Dear Scipion community, > > I have installed Scipion successfully and a number of plugins. > However, the chimera plugin is giving problems. If I install it > via the plugin manager, there are errors. I have tried > uninstalling and reinstalling. If I install it with this command: > > $ scipion3 installp -p scipion-em-chimera > > Then it gives the following output: > Scipion v3.0.9 - Eugenius > Building scipion-em-chimera ... > /home/ubuntu/.conda/envs/scipion3/bin/python -m pip install > scipion-em-chimera==3.1.7 > Collecting scipion-em-chimera==3.1.7 > Using cached scipion_em_chimera-3.1.7-py3-none-any.whl (95 kB) > Requirement already satisfied: scipion-em in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em-chimera==3.1.7) (3.0.13) > Requirement already satisfied: tk-html-widgets in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em-chimera==3.1.7) (0.4.0) > Requirement already satisfied: scipion-pyworkflow>=3.0.15 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-chimera==3.1.7) (3.0.17) > Requirement already satisfied: biopython==1.76 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-chimera==3.1.7) (1.76) > Requirement already satisfied: tifffile in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-chimera==3.1.7) (2021.11.2) > Requirement already satisfied: numpy in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > biopython==1.76->scipion-em->scipion-em-chimera==3.1.7) (1.18.4) > Requirement already satisfied: configparser<=5.0.2 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (5.0.2) > Requirement already satisfied: tkcolorpicker<=2.1.3 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (2.1.3) > Requirement already satisfied: mpi4py<=3.0.3 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (3.0.3) > Requirement already satisfied: psutil<=5.8.0 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (5.8.0) > Requirement already satisfied: matplotlib==3.2.2 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (3.2.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (1.2.0) > Requirement already satisfied: requests<=2.25.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (2.25.1) > Requirement already satisfied: pillow<=8.2.0 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (8.2.0) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (1.3.2) > Requirement already satisfied: > pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (3.0.4) > Requirement already satisfied: cycler>=0.10 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (0.11.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (2.8.2) > Requirement already satisfied: future>=0.16.0 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (0.18.2) > Requirement already satisfied: six>=1.5 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > python-dateutil>=2.1->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (1.16.0) > Requirement already satisfied: chardet<5,>=3.0.2 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (4.0.0) > Requirement already satisfied: urllib3<1.27,>=1.21.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (1.26.7) > Requirement already satisfied: idna<3,>=2.5 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (2.10) > Requirement already satisfied: certifi>=2017.4.17 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (2021.10.8) > Installing collected packages: scipion-em-chimera > Successfully installed scipion-em-chimera-3.1.7 > Done (0.54 seconds) > Building chimerax-1.2.5 ... > Skipping command: wget -nv -c -O > /usr/local/bin/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz> > mv -v /usr/local/bin/scipion/software/em/void.tgz.part > /usr/local/bin/scipion/software/em/void.tgz > All targets exist. > cd /usr/local/bin/scipion/software/em > mkdir /usr/local/bin/scipion/software/em/chimerax-1.2.5 > Skipping command: tar -xf void.tgz -C chimerax-1.2.5 > All targets exist. > Skipping command: cd .. && python > /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/getchimera.py > 1.2.5 > All targets exist. > cd /usr/local/bin/scipion/software/em/chimerax-1.2.5 > cd .. && tar -xf ChimeraX-1.2.5.tar.gz > cd /usr/local/bin/scipion/software/em/chimerax-1.2.5 > mv ../chimerax-1.2.5-rc-2021.05.24/* . > Skipping command: Link 'chimerax-1.2.5 -> chimerax-1.2.5' > All targets exist. > Done (6.28 seconds) > Building scipionchimera-1.3 ... > Skipping command: wget -nv -c -O > /usr/local/bin/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz> > mv -v /usr/local/bin/scipion/software/em/void.tgz.part > /usr/local/bin/scipion/software/em/void.tgz > All targets exist. > cd /usr/local/bin/scipion/software/em > mkdir /usr/local/bin/scipion/software/em/scipionchimera-1.3 > Skipping command: tar -xf void.tgz -C scipionchimera-1.3 > All targets exist. > cd /usr/local/bin/scipion/software/em/scipionchimera-1.3 > --nogui --exit --cmd 'devel install > /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' > && touch installed- > /bin/sh: 1: --nogui: not found > Traceback (most recent call last): > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' > not built (after running ' --nogui --exit --cmd 'devel install > /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' > && touch installed-') > Error at main: target > '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' > not built (after running ' --nogui --exit --cmd 'devel install > /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' > && touch installed-') > > The trouble seems to start with "/bin/sh: 1: --nogui: not found". > I also cannot use chimerax in the GUI. > > I would greatly appreciate your help on this issue. > > Kind regards, > > Lynn Radamaker > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Grigory S. <sha...@gm...> - 2021-11-04 19:10:38
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Hi, I'm pretty sure xmipp works okay (other tests are working), just a few tests have errors which you can ignore (thanks for reporting!). I usually check if xmipp has been compiled properly by importing e.g. 3d volumes of different formats (mrc, spi, hdf5) and make sure I can display them with scipion viewer. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Nov 4, 2021 at 3:57 PM Lynn Radamaker <lyn...@un...> wrote: > Dear Scipion community, > > I'm having some problems with Xmipp. It installed without errors, but it > gives a warning that it cannot find the image library. When I run this test: > > scipion3 tests > pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus > > Then it gives me the following error message: > > [ FAILED ] TestCtfConsensus.test1 > > Traceback (most recent call last): > File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 60, in testPartExecutor > yield > File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 676, in run > self._callTestMethod(testMethod) > File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 633, in _callTestMethod > method() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", > line 186, in test1 > self.checkCTFs(protCTFcons3, > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", > line 71, in checkCTFs > self.assertAlmostEqual(avgCTF['defocusU'], firstCTF.getDefocusU(), > delta=100, > File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 966, in assertAlmostEqual > raise self.failureException(msg) > AssertionError: 24140.0898 != 24025.673242 within 100 delta > (114.4165580000008 difference) : DefocusU doesn't match when defocus > averaging. > > Also, the similar test: > > scipion3 tests pwem.tests.workflows.test_workflow_xmipp > > Gives the error message: > > [ FAILED ] TestXmippWorkflow.testXmippWorkflow > > Traceback (most recent call last): > File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 60, in testPartExecutor > yield > File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 676, in run > self._callTestMethod(testMethod) > File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 633, in _callTestMethod > method() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py", > line 198, in testXmippWorkflow > > self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(), > File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", > line 943, in assertAlmostEqual > diff = abs(first - second) > TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple' > > > > All the other tests (basic and medium) that I ran completed without > problems. I'm hoping that you can give me some advice on how to fix these > error and get Xmipp running properly. > > Kind regards, > > Lynn Radamaker > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Grigory S. <sha...@gm...> - 2021-11-04 19:06:15
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Dear Lynn, it appears you do not have /usr/local/bin/scipion/software/em/chimerax-1.2.5/bin/ChimeraX - main binary file, which means chimerax installation did not work. Have you tried removing /usr/local/bin/scipion/software/em/chimerax* and installing again? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Nov 4, 2021 at 3:57 PM Lynn Radamaker <lyn...@un...> wrote: > Dear Scipion community, > > I have installed Scipion successfully and a number of plugins. However, > the chimera plugin is giving problems. If I install it via the plugin > manager, there are errors. I have tried uninstalling and reinstalling. If I > install it with this command: > > $ scipion3 installp -p scipion-em-chimera > > Then it gives the following output: > Scipion v3.0.9 - Eugenius > Building scipion-em-chimera ... > /home/ubuntu/.conda/envs/scipion3/bin/python -m pip install > scipion-em-chimera==3.1.7 > Collecting scipion-em-chimera==3.1.7 > Using cached scipion_em_chimera-3.1.7-py3-none-any.whl (95 kB) > Requirement already satisfied: scipion-em in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em-chimera==3.1.7) (3.0.13) > Requirement already satisfied: tk-html-widgets in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em-chimera==3.1.7) (0.4.0) > Requirement already satisfied: scipion-pyworkflow>=3.0.15 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-chimera==3.1.7) (3.0.17) > Requirement already satisfied: biopython==1.76 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-chimera==3.1.7) (1.76) > Requirement already satisfied: tifffile in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-chimera==3.1.7) (2021.11.2) > Requirement already satisfied: numpy in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > biopython==1.76->scipion-em->scipion-em-chimera==3.1.7) (1.18.4) > Requirement already satisfied: configparser<=5.0.2 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (5.0.2) > Requirement already satisfied: tkcolorpicker<=2.1.3 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.1.3) > Requirement already satisfied: mpi4py<=3.0.3 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.0.3) > Requirement already satisfied: psutil<=5.8.0 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (5.8.0) > Requirement already satisfied: matplotlib==3.2.2 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.2.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.2.0) > Requirement already satisfied: requests<=2.25.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.25.1) > Requirement already satisfied: pillow<=8.2.0 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (8.2.0) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (1.3.2) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (3.0.4) > Requirement already satisfied: cycler>=0.10 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (0.11.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (2.8.2) > Requirement already satisfied: future>=0.16.0 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (0.18.2) > Requirement already satisfied: six>=1.5 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > python-dateutil>=2.1->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (1.16.0) > Requirement already satisfied: chardet<5,>=3.0.2 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (4.0.0) > Requirement already satisfied: urllib3<1.27,>=1.21.1 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (1.26.7) > Requirement already satisfied: idna<3,>=2.5 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (2.10) > Requirement already satisfied: certifi>=2017.4.17 in > ./.conda/envs/scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) > (2021.10.8) > Installing collected packages: scipion-em-chimera > Successfully installed scipion-em-chimera-3.1.7 > Done (0.54 seconds) > Building chimerax-1.2.5 ... > Skipping command: wget -nv -c -O > /usr/local/bin/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > mv -v /usr/local/bin/scipion/software/em/void.tgz.part > /usr/local/bin/scipion/software/em/void.tgz > All targets exist. > cd /usr/local/bin/scipion/software/em > mkdir /usr/local/bin/scipion/software/em/chimerax-1.2.5 > Skipping command: tar -xf void.tgz -C chimerax-1.2.5 > All targets exist. > Skipping command: cd .. && python > /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/getchimera.py > 1.2.5 > All targets exist. > cd /usr/local/bin/scipion/software/em/chimerax-1.2.5 > cd .. && tar -xf ChimeraX-1.2.5.tar.gz > cd /usr/local/bin/scipion/software/em/chimerax-1.2.5 > mv ../chimerax-1.2.5-rc-2021.05.24/* . > Skipping command: Link 'chimerax-1.2.5 -> chimerax-1.2.5' > All targets exist. > Done (6.28 seconds) > Building scipionchimera-1.3 ... > Skipping command: wget -nv -c -O > /usr/local/bin/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > mv -v /usr/local/bin/scipion/software/em/void.tgz.part > /usr/local/bin/scipion/software/em/void.tgz > All targets exist. > cd /usr/local/bin/scipion/software/em > mkdir /usr/local/bin/scipion/software/em/scipionchimera-1.3 > Skipping command: tar -xf void.tgz -C scipionchimera-1.3 > All targets exist. > cd /usr/local/bin/scipion/software/em/scipionchimera-1.3 > --nogui --exit --cmd 'devel install > /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' > && touch installed- > /bin/sh: 1: --nogui: not found > Traceback (most recent call last): > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' not > built (after running ' --nogui --exit --cmd 'devel install > /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' > && touch installed-') > Error at main: target > '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' not > built (after running ' --nogui --exit --cmd 'devel install > /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' > && touch installed-') > > The trouble seems to start with "/bin/sh: 1: --nogui: not found". I also > cannot use chimerax in the GUI. > > I would greatly appreciate your help on this issue. > > Kind regards, > > Lynn Radamaker > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Lynn R. <lyn...@un...> - 2021-11-04 14:46:39
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Dear Scipion community, I have installed Scipion successfully and a number of plugins. However, the chimera plugin is giving problems. If I install it via the plugin manager, there are errors. I have tried uninstalling and reinstalling. If I install it with this command: $ scipion3 installp -p scipion-em-chimera Then it gives the following output: Scipion v3.0.9 - Eugenius Building scipion-em-chimera ... /home/ubuntu/.conda/envs/scipion3/bin/python -m pip install scipion-em-chimera==3.1.7 Collecting scipion-em-chimera==3.1.7 Using cached scipion_em_chimera-3.1.7-py3-none-any.whl (95 kB) Requirement already satisfied: scipion-em in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em-chimera==3.1.7) (3.0.13) Requirement already satisfied: tk-html-widgets in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em-chimera==3.1.7) (0.4.0) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-chimera==3.1.7) (3.0.17) Requirement already satisfied: biopython==1.76 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-chimera==3.1.7) (1.76) Requirement already satisfied: tifffile in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-chimera==3.1.7) (2021.11.2) Requirement already satisfied: numpy in ./.conda/envs/scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-chimera==3.1.7) (1.18.4) Requirement already satisfied: configparser<=5.0.2 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (5.0.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.1.3) Requirement already satisfied: mpi4py<=3.0.3 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.0.3) Requirement already satisfied: psutil<=5.8.0 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (5.8.0) Requirement already satisfied: matplotlib==3.2.2 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.2.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.25.1) Requirement already satisfied: pillow<=8.2.0 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (8.2.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.3.2) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.0.4) Requirement already satisfied: cycler>=0.10 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (0.11.0) Requirement already satisfied: python-dateutil>=2.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.8.2) Requirement already satisfied: future>=0.16.0 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (0.18.2) Requirement already satisfied: six>=1.5 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.16.0) Requirement already satisfied: chardet<5,>=3.0.2 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (4.0.0) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.26.7) Requirement already satisfied: idna<3,>=2.5 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.10) Requirement already satisfied: certifi>=2017.4.17 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2021.10.8) Installing collected packages: scipion-em-chimera Successfully installed scipion-em-chimera-3.1.7 Done (0.54 seconds) Building chimerax-1.2.5 ... Skipping command: wget -nv -c -O /usr/local/bin/scipion/software/em/void.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz mv -v /usr/local/bin/scipion/software/em/void.tgz.part /usr/local/bin/scipion/software/em/void.tgz All targets exist. cd /usr/local/bin/scipion/software/em mkdir /usr/local/bin/scipion/software/em/chimerax-1.2.5 Skipping command: tar -xf void.tgz -C chimerax-1.2.5 All targets exist. Skipping command: cd .. && python /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/getchimera.py 1.2.5 All targets exist. cd /usr/local/bin/scipion/software/em/chimerax-1.2.5 cd .. && tar -xf ChimeraX-1.2.5.tar.gz cd /usr/local/bin/scipion/software/em/chimerax-1.2.5 mv ../chimerax-1.2.5-rc-2021.05.24/* . Skipping command: Link 'chimerax-1.2.5 -> chimerax-1.2.5' All targets exist. Done (6.28 seconds) Building scipionchimera-1.3 ... Skipping command: wget -nv -c -O /usr/local/bin/scipion/software/em/void.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz mv -v /usr/local/bin/scipion/software/em/void.tgz.part /usr/local/bin/scipion/software/em/void.tgz All targets exist. cd /usr/local/bin/scipion/software/em mkdir /usr/local/bin/scipion/software/em/scipionchimera-1.3 Skipping command: tar -xf void.tgz -C scipionchimera-1.3 All targets exist. cd /usr/local/bin/scipion/software/em/scipionchimera-1.3 --nogui --exit --cmd 'devel install /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' && touch installed- /bin/sh: 1: --nogui: not found Traceback (most recent call last): File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' not built (after running ' --nogui --exit --cmd 'devel install /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' && touch installed-') Error at main: target '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' not built (after running ' --nogui --exit --cmd 'devel install /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' && touch installed-') The trouble seems to start with "/bin/sh: 1: --nogui: not found". I also cannot use chimerax in the GUI. I would greatly appreciate your help on this issue. Kind regards, Lynn Radamaker |
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From: Lynn R. <lyn...@un...> - 2021-11-04 14:46:32
|
Dear Scipion community, I'm having some problems with Xmipp. It installed without errors, but it gives a warning that it cannot find the image library. When I run this test: scipion3 tests pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus Then it gives me the following error message: [ FAILED ] TestCtfConsensus.test1 Traceback (most recent call last): File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor yield File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run self._callTestMethod(testMethod) File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod method() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", line 186, in test1 self.checkCTFs(protCTFcons3, File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", line 71, in checkCTFs self.assertAlmostEqual(avgCTF['defocusU'], firstCTF.getDefocusU(), delta=100, File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 966, in assertAlmostEqual raise self.failureException(msg) AssertionError: 24140.0898 != 24025.673242 within 100 delta (114.4165580000008 difference) : DefocusU doesn't match when defocus averaging. Also, the similar test: scipion3 tests pwem.tests.workflows.test_workflow_xmipp Gives the error message: [ FAILED ] TestXmippWorkflow.testXmippWorkflow Traceback (most recent call last): File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor yield File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run self._callTestMethod(testMethod) File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod method() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py", line 198, in testXmippWorkflow self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(), File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 943, in assertAlmostEqual diff = abs(first - second) TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple' All the other tests (basic and medium) that I ran completed without problems. I'm hoping that you can give me some advice on how to fix these error and get Xmipp running properly. Kind regards, Lynn Radamaker |
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From: Pablo C. <pc...@cn...> - 2021-10-27 08:53:51
|
I think the problem resides in the last image.
You are adding topaz's python to the PATH making it the default python
and that one is taking priority over other pythons, even when activating
environments
Can you make a quick test?
1.- Comment the line in your bash.rc where you are addig topaz to the
PATH variable.
2.- Close the terminal and open it again (or source your bash.rc)
3.- Try to run Scipion3
Alternatively, you might want to modify scipion3 launcher adding a line
to prioritize scipion python?
os.environ["PATH"] = ":".join(["/home/dlsw1/anaconda/envs/scipion3/bin",
os.environ.get("PATH", "")])
Haven't tried it.
On 27/10/21 5:00, #CHEW BING LIANG ALVIN# wrote:
> Dear Scipion community,
>
> I had no issues using scipion3 until I have installed topaz under the
> installation instructions listed in cryosparc
> https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz
> <https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz>
> I have tried reading through the troubleshooting guide but could not
> seem to find a solution to my problem here.
> I have attached various screenshots that show the path pointed out by
> "scipion3" command points to topaz, but this is not the case in my
> bashrc setting. Screenshots *_1 and *_2 are the list of documents in
> the Programme and anaconda env.
> I could not seem to find the scipion.conf file as well, I am unsure if
> setting the scipion.conf is the fix I need in my case or simply
> reinstall scipion3 by following the installation guide again?
>
> Thank you and hope to receive any useful advice on how to proceed.
>
> BestRegards
>
> Alvin CHEW | Ph.D. Student |Nanyang Technological University
> |<http://www.lkcmedicine.ntu.edu.sg/>
>
> /"(You) who (have) a why to live can bear almost any how.//"/
> ~Friedrich Nietzsche
> <http://www.brainyquote.com/quotes/quotes/f/friedrichn103819.html>~
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
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