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[scipion-users] Can't import particles from relion
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From: Tetter S. <tet...@or...> - 2020-11-18 16:02:27
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Dear all,
I have freshly installed Scipion3. When I wanted to import particles from a refinement done in relion3.0, I got an error message. I didn't have Relion installed on the same computer as the Scipion installation, so that sounded reasonable. Thus, I've installed Relion 3.1 manually. Still couldn't import the particles. I've tried to install Relion via the Scipion plugin manager, and everything went well. I've installed relion without the GUI, but I assume that shouldn't be an issue. The installation should be fine:
$ relion_image_handler --version
RELION version: 3.1.1-commit-9f3bf1
Precision: BASE=double
Again, I've tried to import the particles in Scipion, but it still doesn't work:
########################
Protocol validation failed. It usually happens because there are some input missing. Please check if the error message gives you any hint:
Error: Exception
Description:
> error when importing from relion: No module named 'relion.convert'. Relion is needed to import .star files
File "<frozen importlib._bootstrap>", line 991, in findand_load
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
Traceback:
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1878, in validate
childErrors = self._validate()
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocol_import/particles.py", line 245, in validate
ci = self.getImportClass()
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pwem/protocols/protocolimport/particles.py", line 176, in getImportClass
RelionImport = Domain.importFromPlugin('relion.convert', 'RelionImport',
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 294, in importFromPlugin
output = _tryImportFromPlugin(objects)
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 291, in tryImportFromPlugin
Domain._pluginNotFound(plugName, errMsg, doRaise)
File "/home/hilvertg/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/plugin.py", line 437, in __pluginNotFound
raise Exception("\n\n" + raiseMsg)
##############################
Checking for updates as instructed in the error messages gives the following. Curiously, this points to a Relion3.0 installation.
##############################
$ ./scipion3 installp --help --checkUpdates
Scipion v3.0.6 - Eugenius
WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
Warning: Couldn't get remote plugin data for scipion-em-deepfinder
Warning: Couldn't get remote plugin data for scipion-em-tomoj
WARNING: scipion-ed-dials's release 3.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed-dials's release 3.0.1a3 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.0 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.0a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.1 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 0.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
WARNING: scipion-ed's release 3.0.1a2 did not specify a compatible Scipion version. Please, remove this release from pypi
usage: scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]
optional arguments:
-h, --help show help
--noBin Optional flag to install plugins only as a python module,
without installing the plugin binaries. This will affect
all plugins specified in the command.
--checkUpdates Optional flag to check which plugins have new releases.
-p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...]
- pluginName: the name of the plugin to install from the list
of available plugins shown below.
- pluginVersion: (optional) pip version to install. If not specified,
will install the latest compatible with current Scipion.
--devel Optional flag to indicate that we will pass install sources instead
of pip names. Sources might be local paths or git urls. With local
paths, will do pip install -e (editable mode). It is expected to find
the plugin name in the basename of the path or in the repo name.
(i.e. it needs to match the one specified in setup.py). E.g:
scipion installp -p path/to/pluginName --devel
scipion installp -p https://github.com/someOrg/pluginName.git --devel
-j j Number of CPUs to use for compilation
Example: scipion installp -p scipion-em-motioncorr 1.0.6 -p scipion-em-relion -p scipion-em-eman2
Available plugins: ([ ] not installed, [X] seems already installed)
scipion-em 3.0.6 [X]
scipion-em-appion [ ]
scipion-em-atomstructutils [ ]
scipion-em-atsas [ ]
scipion-em-bamfordlab [ ]
scipion-em-bsoft [ ]
scipion-em-ccp4 [ ]
scipion-em-chimera [ ]
scipion-em-cistem [ ]
scipion-em-continuousflex [ ]
scipion-em-cryoassess [ ]
scipion-em-cryodrgn [ ]
scipion-em-cryoef [ ]
scipion-em-cryosparc2 [ ]
scipion-em-deepfinder [ ]
scipion-em-dynamo [ ]
scipion-em-eman2 3.1.1 [X]
scipion-em-empiar [ ]
scipion-em-emxlib [ ]
scipion-em-facilities [ ]
scipion-em-fsc3d [ ]
scipion-em-gautomatch [ ]
scipion-em-gctf [ ]
scipion-em-imagic [ ]
scipion-em-imod [ ]
scipion-em-localrec [ ]
scipion-em-locscale [ ]
scipion-em-motioncorr 1.0.6 [X]
scipion-em-novactf [ ]
scipion-em-phenix [ ]
scipion-em-pyseg [ ]
scipion-em-relion 3.0.0b7 [X]
scipion-em-reliontomo [ ]
scipion-em-resmap [ ]
scipion-em-sidesplitter [ ]
scipion-em-sphire [ ]
scipion-em-spider [ ]
scipion-em-tomo 3.0.6 [X]
scipion-em-tomoj [ ]
scipion-em-topaz [ ]
scipion-em-xmipp 20.7.2 [X]
scipion-em-xmipp2 [ ]
scipion-em-xmipptomo [ ]
###########################################
I am further confused as to why this would point to relion 3.0, even though the final lines in the Scipion plugin manager-based installation seemed to point to the 3.1 version.
###########################################
04565: Building scipion-em-relion ...
04566: /home/hilvertg/anaconda3/envs/.scipion3env/bin/python -m pip install scipion-em-relion==3.0.0b7
04567: Done (1.36 seconds)
04568: Building relion-3.1.0 ...
04569: wget -nv -c -O /home/hilvertg/software/em/relion-3.1.0.tgz.part https://github.com/3dem/relion/archive/3.1.0.tar.gz
04570: mv -v /home/hilvertg/software/em/relion-3.1.0.tgz.part /home/hilvertg/software/em/relion-3.1.0.tgz
04571: cd /home/hilvertg/software/em
04572: tar -xf relion-3.1.0.tgz
04573: cd /home/hilvertg/software/em/relion-3.1.0
04574: cmake -DGUI=OFF -DCMAKE_INSTALL_PREFIX=./ .
04575: cd /home/hilvertg/software/em/relion-3.1.0
04576: make -j 4
04577: Skipping command: Link 'relion-3.1.0 -> relion-3.1.0'
04578: All targets exist.
04579: Done (3 m 57 s)
############################################
Any idea what I need to do to import my particles?
Thanks,
Stephan
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