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[scipion-users] relion postprocessing error
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From: Dmitry A. S. <sem...@gm...> - 2021-07-29 21:47:27
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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><span lang=EN-GB>Dear colleagues,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>The issue with relion postprocessing (please see below)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Any suggestions?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thank you<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Dmitry<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=RU><o:p> </o:p></span></p><p class=MsoNormal><span lang=RU><o:p> </o:p></span></p><p class=MsoNormal><span lang=RU>00009: runMode: Restart<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00010: MPI: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00011: threads: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00012: Starting at step: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00013: Running steps <o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00014: STARTED: convertInputStep, step 1, time 2021-07-29 23:44:34.952023<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00015: /bin/sh: -c: line 0: syntax error near unexpected token `('<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00016: /bin/sh: -c: line 0: ` relion_image_handler --i Runs/009364_ProtImportMask/extra/cryosparc_P17_J22_009_volume_mask_refine(1).mrc --o Runs/009432_ProtRelionPostprocess/input/input_mask.mrc --angpix 0.59200 --rescale_angpix 0.59200 --new_box 320 --threshold_above 1 --threshold_below 0'<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00017: ** Running command: relion_image_handler --i Runs/009364_ProtImportMask/extra/cryosparc_P17_J22_009_volume_mask_refine(1).mrc --o Runs/009432_ProtRelionPostprocess/input/input_mask.mrc --angpix 0.59200 --rescale_angpix 0.59200 --new_box 320 --threshold_above 1 --threshold_below 0<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00018: Traceback (most recent call last):<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00019: File "/usr/local/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 lang=RU>00020: self._run()<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00021: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00022: resultFiles = self._runFunc()<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00023: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00024: return self._func(*self._args)<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00025: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_postprocess.py", line 199, in convertInputStep<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00026: convert.convertMask(self.solventMask.get(),<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00027: File "/usr/local/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 lang=RU>00028: pwutils.runJob(None, 'relion_image_handler', params, env=Plugin.getEnviron())<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00029: File "/usr/local/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 lang=RU>00030: return runCommand(command, env, cwd)<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00031: File "/usr/local/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 lang=RU>00032: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00033: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00034: raise CalledProcessError(retcode, cmd)<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00035: subprocess.CalledProcessError: Command ' relion_image_handler --i Runs/009364_ProtImportMask/extra/cryosparc_P17_J22_009_volume_mask_refine(1).mrc --o Runs/009432_ProtRelionPostprocess/input/input_mask.mrc --angpix 0.59200 --rescale_angpix 0.59200 --new_box 320 --threshold_above 1 --threshold_below 0' returned non-zero exit status 1.<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00036: Protocol failed: Command ' relion_image_handler --i Runs/009364_ProtImportMask/extra/cryosparc_P17_J22_009_volume_mask_refine(1).mrc --o Runs/009432_ProtRelionPostprocess/input/input_mask.mrc --angpix 0.59200 --rescale_angpix 0.59200 --new_box 320 --threshold_above 1 --threshold_below 0' returned non-zero exit status 1.<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00037: FAILED: convertInputStep, step 1, time 2021-07-29 23:44:35.022128<o:p></o:p></span></p><p class=MsoNormal><span lang=RU>00038: *** Last status is failed</span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
