From: Grigory S. <sha...@gm...> - 2020-11-25 09:30:38
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Hi Colin, it looks like an error with reading the converted reference volume. Do you have the mrc volume in Runs/006157_ProtRelionRefine3D/tmp 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 Wed, Nov 25, 2020 at 5:30 AM <pc...@cn...> wrote: > Hi Collin, > > Could you send us Runs/004006_ProtUserSubSet/particles.sqlite > > Meanwhile, try to update relion plugin too. > > > El 25 nov. 2020 1:12, Colin Deniston <ckd...@gm...> escribió: > > I'm getting this error only when I try and run either a relion 3D refine > or 3D classification job in scipion on a specific workstation. Any idea > where the issue may be? I'm updating to the most recent version of scipion > now to see if it will fix, I currently have 3.0.5. Thanks! > > STARTED: convertInputStep, step 1, time 2020-11-24 16:07:15.402676 > 00019: Converting set from 'Runs/004006_ProtUserSubSet/particles.sqlite' > into 'Runs/006157_ProtRelionRefine3D/input_particles.star' > 00020: convertBinaryFiles: creating soft links. > 00021: Root: Runs/006157_ProtRelionRefine3D/extra/input -> > Runs/000961_ProtRelionExtractParticles/extra > 00022: Traceback (most recent call last): > 00023: File > "/apps/GNU/scipion/3.0/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 188, in run > 00024: self._run() > 00025: File > "/apps/GNU/scipion/3.0/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 239, in _run > 00026: resultFiles = self._runFunc() > 00027: File > "/apps/GNU/scipion/3.0/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 235, in _runFunc > 00028: return self._func(*self._args) > 00029: File > "/home/cdeniston/.local/lib/python3.8/site-packages/relion/protocols/protocol_base.py", > line 803, in convertInputStep > 00030: self._convertRef() > 00031: File > "/home/cdeniston/.local/lib/python3.8/site-packages/relion/protocols/protocol_base.py", > line 1226, in _convertRef > 00032: self._convertVol(ih, refVols[0]) > 00033: File > "/home/cdeniston/.local/lib/python3.8/site-packages/relion/protocols/protocol_base.py", > line 1210, in _convertVol > 00034: img = ih.read(inputVol) > 00035: File > "/apps/GNU/scipion/3.0/lib/python3.8/site-packages/pwem/emlib/image/image_handler.py", > line 275, in read > 00036: return self._imgClass(location) > 00037: TypeError: __init__() takes 1 positional argument but 2 were given > 00038: Protocol failed: __init__() takes 1 positional argument but 2 > were given > 00039: FAILED: convertInputStep, step 1, time 2020-11-24 16:07:29.782580 > 00040: *** Last status is failed > 00041: ------------------- PROTOCOL FAILED (DONE 1/3) > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |