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

[<pc...@cn...>]

<div dir='auto'><div>Hi Collin,&nbsp;<div dir="auto"><br></div><div dir="auto">Could you send us&nbsp;<span style="font-family: sans-serif; font-size: 12.8px;">Runs/004006_ProtUserSubSet/particles.sqlite</span></div><div dir="auto"><span style="font-family: sans-serif; font-size: 12.8px;"><br></span></div><div dir="auto"><span style="font-family: sans-serif; font-size: 12.8px;">Meanwhile, try to update relion plugin too.</span></div><br><div class="gmail_extra"><br><div class="gmail_quote">El 25 nov. 2020 1:12, Colin Deniston &lt;ckd...@gm...&gt; escribió:<br type="attribution"><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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!<div><br></div><div>STARTED: convertInputStep, step 1, time 2020-11-24 16:07:15.402676<br>00019: &nbsp; Converting set from 'Runs/004006_ProtUserSubSet/particles.sqlite' into 'Runs/006157_ProtRelionRefine3D/input_particles.star'<br>00020: &nbsp; convertBinaryFiles: creating soft links.<br>00021: &nbsp; &nbsp; &nbsp;Root: Runs/006157_ProtRelionRefine3D/extra/input -&gt; Runs/000961_ProtRelionExtractParticles/extra<br>00022: &nbsp; Traceback (most recent call last):<br>00023: &nbsp; &nbsp; File "/apps/GNU/scipion/3.0/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 188, in run<br>00024: &nbsp; &nbsp; &nbsp; self._run()<br>00025: &nbsp; &nbsp; File "/apps/GNU/scipion/3.0/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 239, in _run<br>00026: &nbsp; &nbsp; &nbsp; resultFiles = self._runFunc()<br>00027: &nbsp; &nbsp; File "/apps/GNU/scipion/3.0/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 235, in _runFunc<br>00028: &nbsp; &nbsp; &nbsp; return self._func(*self._args)<br>00029: &nbsp; &nbsp; File "/home/cdeniston/.local/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 803, in convertInputStep<br>00030: &nbsp; &nbsp; &nbsp; self._convertRef()<br>00031: &nbsp; &nbsp; File "/home/cdeniston/.local/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 1226, in _convertRef<br>00032: &nbsp; &nbsp; &nbsp; self._convertVol(ih, refVols[0])<br>00033: &nbsp; &nbsp; File "/home/cdeniston/.local/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 1210, in _convertVol<br>00034: &nbsp; &nbsp; &nbsp; img = ih.read(inputVol)<br>00035: &nbsp; &nbsp; File "/apps/GNU/scipion/3.0/lib/python3.8/site-packages/pwem/emlib/image/image_handler.py", line 275, in read<br>00036: &nbsp; &nbsp; &nbsp; return self._imgClass(location)<br>00037: &nbsp; TypeError: __init__() takes 1 positional argument but 2 were given<br>00038: &nbsp; Protocol failed: __init__() takes 1 positional argument but 2 were given<br>00039: &nbsp; FAILED: convertInputStep, step 1, time 2020-11-24 16:07:29.782580<br>00040: &nbsp; *** Last status is failed <br>00041: &nbsp; ------------------- PROTOCOL FAILED (DONE 1/3)<br></div></div>
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