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[scipion-users] Bayesian polishing issue
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From: Dmitry S. <sem...@gm...> - 2020-12-28 22:16:34
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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"><div class=WordSection1><div><p class=MsoNormal><span lang=EN-US>Dear colleagues,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><u><span lang=EN-US>Bayesian polishing issue –<o:p></o:p></span></u></p><p class=MsoNormal><u><span lang=EN-US><o:p><span style='text-decoration:none'> </span></o:p></span></u></p><p class=MsoNormal><u><span lang=EN-US><o:p><span style='text-decoration:none'> </span></o:p></span></u></p><p class=MsoNormal><span lang=EN-US>00008: workingDir: Runs/004138_ProtRelionBayesianPolishing<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00009: runMode: Restart<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00010: MPI: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00011: threads: 14<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00012: Starting at step: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00013: Running steps <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00014: STARTED: convertInputStep, step 1, time 2020-12-28 23:03:24.304754<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00015: Converting set from 'Runs/003937_ProtRelionRefine3D/particles.sqlite' into 'Runs/004138_ProtRelionBayesianPolishing/input_particles.star'<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00016: convertBinaryFiles: creating soft links.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00017: Root: Runs/004138_ProtRelionBayesianPolishing/input/particles/input -> Runs/000427_ProtRelionExtractParticles/extra<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00018: FINISHED: convertInputStep, step 1, time 2020-12-28 23:04:33.416996<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00019: STARTED: trainOrPolishStep, step 2, time 2020-12-28 23:04:33.422574<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00020: relion_motion_refine --i Runs/004138_ProtRelionBayesianPolishing/input_particles.star --o Runs/004138_ProtRelionBayesianPolishing/extra --f Runs/004089_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004138_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 3 --last_frame 0 --min_p 421029 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00021: + Reading Runs/004138_ProtRelionBayesianPolishing/input_particles.star..<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00022: in: /home/user/Data/Software/Scipion3/software/em/relion-3.1.0/src/jaz/micrograph_handler.cpp, line 261<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00023: ERROR: <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00024: There is no movie metadata STAR file for any micrographs!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00025: === Backtrace ===<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00026: relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x453571]<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00027: relion_motion_refine(_ZN17MicrographHandler11loadInitialERKSt6vectorI13MetaDataTableSaIS1_EEbRiRdRSs+0xb95) [0x531275]<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00028: relion_motion_refine(_ZN17MicrographHandler4initERKSt6vectorI13MetaDataTableSaIS1_EEbiRiRdRSs+0x78) [0x533a88]<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00029: relion_motion_refine(_ZN13MotionRefiner4initEv+0x546) [0x47d1a6]<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00030: relion_motion_refine(main+0x31) [0x428841]<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00031: /lib64/libc.so.6(__libc_start_main+0xf5) [0x7ff26cfb7555]<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00032: relion_motion_refine() [0x42955f]<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00033: ==================<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00034: ERROR: <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00035: There is no movie metadata STAR file for any micrographs!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00036: Traceback (most recent call last):<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00037: 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>00038: self._run()<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00039: 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>00040: resultFiles = self._runFunc()<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00041: 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>00042: return self._func(*self._args)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00043: 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>00044: self.runJob(prog, args)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00045: 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>00046: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00047: 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>00048: process.runJob(log, programName, params,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00049: 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>00050: return runCommand(command, env, cwd)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00051: 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>00052: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00053: 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>00054: raise CalledProcessError(retcode, cmd)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00055: subprocess.CalledProcessError: Command 'relion_motion_refine --i Runs/004138_ProtRelionBayesianPolishing/input_particles.star --o Runs/004138_ProtRelionBayesianPolishing/extra --f Runs/004089_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004138_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 3 --last_frame 0 --min_p 421029 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00056: Protocol failed: Command 'relion_motion_refine --i Runs/004138_ProtRelionBayesianPolishing/input_particles.star --o Runs/004138_ProtRelionBayesianPolishing/extra --f Runs/004089_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004138_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 3 --last_frame 0 --min_p 421029 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00057: FAILED: trainOrPolishStep, step 2, time 2020-12-28 23:04:45.953315<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00058: *** Last status is failed <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>00059: ------------------- PROTOCOL FAILED (DONE 2/2)<hr align=left size=1 width="33%"><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>Any ideas?<o:p></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> </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></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
