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[scipion-users] relion 3D auto refinement error (after Bayesian polishing)
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From: Dmitry A. S. <sem...@gm...> - 2021-07-10 14:47:17
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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:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal>Dear Grigory & colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>During relion 3D refinement I received the error – please see below.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Prehistory – I run the Bayesian polishing with the relion 3D refinement dataset (<span style='color:#0070C0'>syntax error near unexpected token `('</span>).<span style='color:#0070C0'><o:p></o:p></span></p><p class=MsoNormal>I suspect there are some errors in Bayesian polishing outcome dataset. Some of them I fixed by deleting black images.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>So the question is how to fix the remaining errors to let the relion 3D refinement run?</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you in advance,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</p><p class=MsoNormal>Dmitry</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='color:#0070C0'>RUNNING PROTOCOL -----------------<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00002: Hostname: localhost4.localdomain4<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00003: PID: 86173<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00004: pyworkflow: 3.0.16<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00005: plugin: relion<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00006: plugin v: 3.1.2<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00007: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00008: workingDir: Runs/065340_ProtRelionRefine3D<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00009: runMode: Continue<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00010: MPI: 7<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00011: threads: 6<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00012: /bin/sh: -c: line 0: syntax error near unexpected token `('<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00013: /bin/sh: -c: line 0: ` relion_image_handler --i Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc --o Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1 --threshold_below 0'<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00014: ** Running command: relion_image_handler --i Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc --o Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1 --threshold_below 0<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00015: Traceback (most recent call last):<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00016: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00017: self._run()<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00018: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1361, in _run<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00019: self._insertAllSteps() # Define steps for execute later<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00020: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 740, in _insertAllSteps<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00021: self._insertRelionStep()<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00022: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 751, in _insertRelionStep<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00023: self._setNormalArgs(args)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00024: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 969, in _setNormalArgs<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00025: self._setBasicArgs(args)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00026: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 1038, in _setBasicArgs<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00027: self._setMaskArgs(args)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00028: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 1065, in _setMaskArgs<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00029: mask = relion.convert.convertMask(self.referenceMask.get(),<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00030: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/convert_utils.py", line 224, in convertMask<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00031: pwutils.runJob(None, 'relion_image_handler', params, env=Plugin.getEnviron())<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00032: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00033: return runCommand(command, env, cwd)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00034: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00035: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00036: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00037: raise CalledProcessError(retcode, cmd)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00038: subprocess.CalledProcessError: Command ' relion_image_handler --i Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc --o Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1 --threshold_below 0' returned non-zero exit status 1.<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>00039: ------------------- PROTOCOL FAILED (DONE 0/0) <o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
