Re: [scipion-users] Error running relion 3D refinement jobs on one of my workstations

[Grigory S. <sha...@gm...>]

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)
>
>
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