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[scipion-users] relion Bayesian polishing -- Signals.SIGKILL: 9 error
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From: Dmitry S. <sem...@gm...> - 2021-01-01 17:04:57
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:612.0pt 792.0pt; margin:2.0cm 42.5pt 2.0cm 3.0cm;} div.WordSection1 {page:WordSection1;} --></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 & Grigory,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Happy new year!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Once again the issue with relion Bayesian polishing.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I have 421029 particles that I would like to apply for Bayesian polishing (training) protocol.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>But every time this step collapses with the following error + Signals.SIGKILL: 9 (please see below).<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I suspect that the problem can be in too large number of particles.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>What is your opinion?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>If that is an issue how still is it possible to run this Bayesian polishing (training) protocol?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><br>Thank you!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </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> </o:p></span></p><p class=MsoNormal><span lang=EN-US>=============================================================================================================<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>02234: 1985: GridSquare_11360233_Data_FoilHole_13166836_Data_11396369_11396371_20201215_204224_Fractions.mrc<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02235: 1404: GridSquare_11359542_Data_FoilHole_11378215_Data_11396369_11396371_20201214_055446_Fractions.mrc<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02236: 361: GridSquare_11359008_Data_FoilHole_11380461_Data_11396369_11396371_20201214_181814_Fractions.mrc<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02237: <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02238: + 421029 particles found in 2199 micrographs<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02239: + preparing alignment data... <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02240: Traceback (most recent call last):<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02241: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 189, in run<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02242: self._run()<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02243: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02244: resultFiles = self._runFunc()<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02245: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02246: return self._func(*self._args)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02247: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 309, in trainOrPolishStep<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02248: self.runJob(prog, args)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02249: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1357, in runJob<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02250: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02251: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02252: process.runJob(log, programName, params,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02253: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 51, in runJob<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02254: return runCommand(command, env, cwd)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02255: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 66, in runCommand<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02256: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02257: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", line 364, in check_call<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02258: raise CalledProcessError(retcode, cmd)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02259: subprocess.CalledProcessError: Command 'relion_motion_refine --i Runs/006095_ProtRelionBayesianPolishing/input_particles.star --o Runs/006095_ProtRelionBayesianPolishing/extra --f Runs/006046_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/006095_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 3 --last_frame 20 --min_p 421029 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02260: Protocol failed: Command 'relion_motion_refine --i Runs/006095_ProtRelionBayesianPolishing/input_particles.star --o Runs/006095_ProtRelionBayesianPolishing/extra --f Runs/006046_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/006095_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 3 --last_frame 20 --min_p 421029 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02261: FAILED: trainOrPolishStep, step 2, time 2021-01-01 13:40:51.032080<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>02262: *** Last status is failed<o:p></o:p></span></p></div></body></html> |
