[scipion-users] Bayesian polishing

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--></style></head><body lang=RU link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Dear colleagues,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US>The issue with Bayesian polishing – <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>Logging configured. STDOUT --&gt; Runs/003279_ProtRelionBayesianPolishing/logs/run.stdout , STDERR --&gt; Runs/003279_ProtRelionBayesianPolishing/logs/run.stderr<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[32mRUNNING PROTOCOL -----------------[0m<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>Protocol starts<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>Hostname: localhost4.localdomain4<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>PID: 240224<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>pyworkflow: 3.0.17<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>plugin: relion<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>plugin v: 3.1.3<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>workingDir: Runs/003279_ProtRelionBayesianPolishing<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>runMode: Continue<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>          MPI: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>      threads: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'> Starting at step: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'> Running steps <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[35mSTARTED[0m: convertInputStep, step 1, time 2021-09-02 21:31:33.074480<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>Converting set from 'Runs/002848_ProtCryoSparcNonUniformRefine3D/particles.sqlite' into 'Runs/003279_ProtRelionBayesianPolishing/input_particles.star'<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[31mProtocol failed: list index out of range[0m<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[35mFAILED[0m: convertInputStep, step 1, time 2021-09-02 21:31:33.532782<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>*** Last status is failed <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[32m------------------- PROTOCOL FAILED (DONE 1/2)[0m<o:p></o:p></span></p><div style='mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;padding:0cm 0cm 1.0pt 0cm'><p class=MsoNormal style='border:none;padding:0cm'><o:p>&nbsp;</o:p></p></div><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><span style='color:#0070C0'>Traceback (most recent call last):<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>  File &quot;/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py&quot;, line 201, in run<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>    self._run()<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>  File &quot;/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py&quot;, line 252, in _run<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>    resultFiles = self._runFunc()<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>  File &quot;/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py&quot;, line 248, in _runFunc<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>    return self._func(*self._args)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>  File &quot;/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py&quot;, line 296, in convertInputStep<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>    tableShifts.addRow(i, shiftsX[i-a0] + xoff,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>IndexError: list index out of range<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[31mProtocol failed: list index out of range[0m</span></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><span lang=EN-US>Any idea?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US>Thank you<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Dmitry<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US>P.s. also strange behavior of adding movies to the project – the process just hangs without finishing.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US>Could those 2 issues be connected?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Could that happened after the SCIPION3 updates?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><o:p>&nbsp;</o:p></p></div></body></html>

[scipion-users] Bayesian polishing

Image processing framework to integrate EM software packages.

[scipion-users] Bayesian polishing