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From: Pablo C. <pc...@cn...> - 2021-08-04 13:07:01
|
Hi! I do not see an straight way to do that. Having a 3d map probably I'd go for template based pickings? On 4/8/21 11:25, Dmitry Semchonok wrote: > Dear colleagues, > > Small question — > > Is it possible to make shire cryolo training model from the available 3D cryo-em map? > > > Thank you > > Sincerely, > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Carlos O. S. <co...@cn...> - 2021-08-04 11:02:12
|
Hi Dmitry, there is a protocol called "resolution 3d" that can compare two volumes at the level of FSC and DPR. Otherwise, there are also two protocols "volumes adjust" and "volumes subtraction" that adapt 1 to 2 as much as possible (the definition of this is now under review) before subtracting. You have also "align volume" in case they are not exactly in the same position. And the box size and voxel size can be adapted with "Crop/resize". Cheers, Carlos Oscar On 8/4/21 11:57 AM, Dmitry Semchonok wrote: > Dear colleagues, > > What are the tools for the 3D map comparison in SCIPION? > > > Briefly: > I have a map of about 5A that I wanted to compare with the published map of about 3A resolution. > > What is the best way to do that? > > > > Thanks a lot > > > > Sincerely, > Dmitry > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Dmitry S. <Sem...@gm...> - 2021-08-04 09:57:21
|
Dear colleagues, What are the tools for the 3D map comparison in SCIPION? Briefly: I have a map of about 5A that I wanted to compare with the published map of about 3A resolution. What is the best way to do that? Thanks a lot Sincerely, Dmitry |
|
From: Dmitry S. <Sem...@gm...> - 2021-08-04 09:40:16
|
Dear colleagues, The shire cryolo picking ends up after few micrographs picking with the following error: INISHED: pickMicrographListStep, step 9, time 2021-08-04 11:38:10.274708 00762: Reading coordinates from mics: 81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128 00763: Traceback (most recent call last): 00764: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/convert.py", line 100, in iterCoords 00765: if self._getDataLength() == 7: # crYOLO generates .cbox files with 7 columns from version > 1.5.4 00766: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/convert.py", line 92, in _getDataLength 00767: head = next(self._file) # Read the first line 00768: StopIteration 00769: 00770: The above exception was the direct cause of the following exception: 00771: 00772: Traceback (most recent call last): 00773: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run 00774: self._run() 00775: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1367, in _run 00776: self._runSteps(startIndex) 00777: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1218, in _runSteps 00778: self._stepsExecutor.runSteps(self._steps, 00779: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 131, in runSteps 00780: stepsCheckCallback() 00781: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 301, in _stepsCheck 00782: self._checkNewOutput() 00783: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 400, in _checkNewOutput 00784: newDoneUpdated = self._updateOutputCoordSet(newDone, streamMode) 00785: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 462, in _updateOutputCoordSet 00786: self.readCoordsFromMics(outputDir, micDoneList, outputCoords) 00787: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/protocols/protocol_cryolo_picking.py", line 236, in readCoordsFromMics 00788: convert.readMicrographCoords(mic, outputCoords, coordsFile, boxSize, 00789: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/convert.py", line 182, in readMicrographCoords 00790: for x, y, score in reader.iterCoords(): 00791: RuntimeError: generator raised StopIteration 00792: ------------------- PROTOCOL FAILED (DONE 9/1615) Any suggestion? Thank you Sincerely, Dmitry |
|
From: Dmitry S. <Sem...@gm...> - 2021-08-04 09:26:17
|
Dear colleagues, Small question — Is it possible to make shire cryolo training model from the available 3D cryo-em map? Thank you Sincerely, Dmitry |
|
From: Dmitry S. <Sem...@gm...> - 2021-07-30 07:15:58
|
Dear Pablo,
Thanks - indeed I tried that yesterday and everything worked out.
Sincerely,
Dmitry
> On 30. Jul 2021, at 09:03, Pablo Conesa <pc...@cn...> wrote:
>
> Hi Dmitry, probably that (1) in the mask name is causing the error.
>
> Rename it, remove the (), and might work.
>
>
>
> On 29/7/21 23:47, Dmitry A. Semchonok wrote:
>> Dear colleagues,
>>
>> The issue with relion postprocessing (please see below)
>>
>> Any suggestions?
>>
>> Thank you
>>
>> Sincerely,
>> Dmitry
>>
>>
>>
>> 00009: runMode: Restart
>> 00010: MPI: 1
>> 00011: threads: 1
>> 00012: Starting at step: 1
>> 00013: Running steps
>> 00014: STARTED: convertInputStep, step 1, time 2021-07-29 23:44:34.952023
>> 00015: /bin/sh: -c: line 0: syntax error near unexpected token `('
>> 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'
>> 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
>> 00018: Traceback (most recent call last):
>> 00019: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run
>> 00020: self._run()
>> 00021: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run
>> 00022: resultFiles = self._runFunc()
>> 00023: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc
>> 00024: return self._func(*self._args)
>> 00025: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_postprocess.py", line 199, in convertInputStep
>> 00026: convert.convertMask(self.solventMask.get(),
>> 00027: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/convert_utils.py", line 224, in convertMask
>> 00028: pwutils.runJob(None, 'relion_image_handler', params, env=Plugin.getEnviron())
>> 00029: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
>> 00030: return runCommand(command, env, cwd)
>> 00031: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
>> 00032: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
>> 00033: File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
>> 00034: raise CalledProcessError(retcode, cmd)
>> 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.
>> 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.
>> 00037: FAILED: convertInputStep, step 1, time 2021-07-29 23:44:35.022128
>> 00038: *** Last status is failed
>>
>>
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li... <mailto:sci...@li...>
>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>
> --
> Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es/> team
> _______________________________________________
> scipion-users mailing list
> sci...@li... <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>
|
|
From: Pablo C. <pc...@cn...> - 2021-07-30 07:03:29
|
Hi Dmitry, probably that (1) in the mask name is causing the error.
Rename it, remove the (), and might work.
On 29/7/21 23:47, Dmitry A. Semchonok wrote:
>
> Dear colleagues,
>
> The issue with relion postprocessing (please see below)
>
> Any suggestions?
>
> Thank you
>
> Sincerely,
>
> Dmitry
>
> 00009: runMode: Restart
>
> 00010: MPI: 1
>
> 00011: threads: 1
>
> 00012: Starting at step: 1
>
> 00013: Running steps
>
> 00014: STARTED: convertInputStep, step 1, time 2021-07-29
> 23:44:34.952023
>
> 00015: /bin/sh: -c: line 0: syntax error near unexpected token `('
>
> 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'
>
> 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
>
> 00018: Traceback (most recent call last):
>
> 00019: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
>
> 00020: self._run()
>
> 00021: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 248, in _run
>
> 00022: resultFiles = self._runFunc()
>
> 00023: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 244, in _runFunc
>
> 00024: return self._func(*self._args)
>
> 00025: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_postprocess.py",
> line 199, in convertInputStep
>
> 00026: convert.convertMask(self.solventMask.get(),
>
> 00027: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/convert_utils.py",
> line 224, in convertMask
>
> 00028: pwutils.runJob(None, 'relion_image_handler', params,
> env=Plugin.getEnviron())
>
> 00029: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
>
> 00030: return runCommand(command, env, cwd)
>
> 00031: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
>
> 00032: check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
>
> 00033: File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line
> 364, in check_call
>
> 00034: raise CalledProcessError(retcode, cmd)
>
> 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.
>
> 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.
>
> 00037: FAILED: convertInputStep, step 1, time 2021-07-29 23:44:35.022128
>
> 00038: *** Last status is failed
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Dmitry A. S. <sem...@gm...> - 2021-07-29 22:04:35
|
<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;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .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 solution was simple – when I downloaded the mask several times and selected ANYone with the brackets (X), where X is the number of downloads of this mask. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>This step will lead to such error.<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>So the solution – the input mask in relion postprocessing should not contain the ( ) symbols.<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><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=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
|
From: Dmitry A. S. <sem...@gm...> - 2021-07-29 21:47:27
|
<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> |
|
From: Grigory S. <sha...@gm...> - 2021-07-28 12:07:51
|
Hi,
please check:
1) _rlnMicrographName in input_particles.star and
input_corrected_micrographs.star
match
2) you have _rlnMicrographMetadata star files that contain correct
information
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...
On Mon, Jul 26, 2021 at 8:56 PM Dmitry A. Semchonok <sem...@gm...>
wrote:
> Dear colleagues,
>
>
>
> Issue with Bayesian polishing.
>
>
>
> The error says that the metadata was not found, my understanding is that
> original files are not on the place but currently this is not the case.
>
> Would you please prompt what can case the issue?
>
>
>
> Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
> Hostname: cryoem01
>
> PID: 37775
>
> pyworkflow: 3.0.16
>
> plugin: relion
>
> plugin v: 3.1.2
>
> currentDir: /data1/ScipionUserData/projects/20201211_apof_ph5_pos4
>
> workingDir: Runs/009050_ProtRelionBayesianPolishing
>
> runMode: Continue
>
> MPI: 1
>
> threads: 1
>
> Starting at step: 1
>
> Running steps
>
> [35mSTARTED[0m: convertInputStep, step 1, time 2021-07-26 21:49:10.454974
>
> Converting set from
> 'Runs/008377_ProtCryoSparcNewNonUniformRefine3D/particles.sqlite' into
> 'Runs/009050_ProtRelionBayesianPolishing/input_particles.star'
>
> convertBinaryFiles: creating soft links.
>
> Root: Runs/009050_ProtRelionBayesianPolishing/input/particles/input ->
> Runs/000427_ProtRelionExtractParticles/extra
>
> [35mFINISHED[0m: convertInputStep, step 1, time 2021-07-26 21:49:56.565214
>
> [35mSTARTED[0m: trainOrPolishStep, step 2, time 2021-07-26 21:49:56.684070
>
> [32m relion_motion_refine --i
> Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/009050_ProtRelionBayesianPolishing/extra --f
> Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac
> 0.500 --params3 --j 1 [0m
>
> + Reading Runs/009050_ProtRelionBayesianPolishing/input_particles.star...
>
> in: /opt/Scipion3/software/em/relion-3.1.2/src/jaz/micrograph_handler.cpp,
> line 264
>
> ERROR:
>
> There is no movie metadata STAR file for any micrographs!
>
> === Backtrace ===
>
> relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x47e9d1]
>
> relion_motion_refine(_ZN17MicrographHandler11loadInitialERKSt6vectorI13MetaDataTableSaIS1_EEbRiRdRSs+0xa60)
> [0x582890]
>
> relion_motion_refine(_ZN17MicrographHandler4initERKSt6vectorI13MetaDataTableSaIS1_EEbiRiRdRSs+0x78)
> [0x585fc8]
>
> relion_motion_refine(_ZN13MotionRefiner4initEv+0x516) [0x5077d6]
>
> relion_motion_refine(main+0x31) [0x440391]
>
> /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f653431f555]
>
> relion_motion_refine() [0x444570]
>
> ==================
>
> ERROR:
>
> There is no movie metadata STAR file for any micrographs!
>
> Traceback (most recent call last):
>
> File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
>
> self._run()
>
> File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 248, in _run
>
> resultFiles = self._runFunc()
>
> File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 244, in _runFunc
>
> return self._func(*self._args)
>
> File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py",
> line 351, in trainOrPolishStep
>
> self.runJob(self._getProgram('relion_motion_refine'), args)
>
> File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1389, in runJob
>
> self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
>
> File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
>
> process.runJob(log, programName, params,
>
> File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
>
> return runCommand(command, env, cwd)
>
> File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
>
> check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
>
> File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py",
> line 364, in check_call
>
> raise CalledProcessError(retcode, cmd)
>
> subprocess.CalledProcessError: Command ' relion_motion_refine --i
> Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/009050_ProtRelionBayesianPolishing/extra --f
> Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac
> 0.500 --params3 --j 1 ' returned non-zero exit status 1.
>
> [31mProtocol failed: Command ' relion_motion_refine --i
> Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/009050_ProtRelionBayesianPolishing/extra --f
> Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac
> 0.500 --params3 --j 1 ' returned non-zero exit status 1.[0m
>
> [35mFAILED[0m: trainOrPolishStep, step 2, time 2021-07-26 21:50:07.277034
>
> *** Last status is failed
>
> [32m------------------- PROTOCOL FAILED (DONE 2/2)[0m
>
>
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Dmitry A. S. <sem...@gm...> - 2021-07-28 11:54:22
|
Dear Grigory, Thank you for your suggestion! This is one more option that we are exploring 🙂 Would you perhaps know what causing the issue with bayesian polishing ? It seems that the software can not see the metadata (which is correctly placed) Thank you! Sincerely, Dmitry On July 28, 2021 12:52:06 PM Grigory Sharov <sha...@gm...> wrote: > Hi Dmitry, > > Dear colleagues, > > Is there an official fix released already for the renaming the destination > where original files are located? > I plan to do the Bayesian polishing but my original files have different > location then previously. > > > > You can create a symbolic link for the folder with movies that matches the > old location. > > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > e-mail: gs...@mr... > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Grigory S. <sha...@gm...> - 2021-07-28 10:51:55
|
Hi Dmitry, Dear colleagues, > > Is there an official fix released already for the renaming the destination > where original files are located? > I plan to do the Bayesian polishing but my original files have different > location then previously. You can create a symbolic link for the folder with movies that matches the old location. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... |
|
From: Dmitry S. <sem...@gm...> - 2021-07-28 04:37:24
|
<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:Helvetica; panose-1:2 11 5 4 2 2 2 2 2 4;} @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;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} pre {mso-style-priority:99; mso-style-link:"HTML Preformatted Char"; margin:0in; margin-bottom:.0001pt; font-size:10.0pt; font-family:"Courier New";} span.HTMLPreformattedChar {mso-style-name:"HTML Preformatted Char"; mso-style-priority:99; mso-style-link:"HTML Preformatted"; font-family:"Courier New";} span.apple-converted-space {mso-style-name:apple-converted-space;} .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 Pablo,<o:p></o:p></p><div><div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you for this update – yes I understand that it works for the input data only.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>My current problem seems to be connected to the Bayesian polishing – when relion protocol (in SCIPION) complains on the absence of the metadata that if fact is present.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Do you or Grigory have solution for that issue?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,<o:p></o:p></p><p class=MsoNormal>Dmitry<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On 27. Jul 2021, at 09:31, Pablo Conesa <pc...@cn...> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>Dear Dmitry, let me clarify that in this case is not a fix but a feature: If you've moved the movies, paths are broken, and therefore, bugs happens.<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>I think we planned to release something like: "scipion3 fixlinks ..." but is not done.<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>If you still need this, let me know we can prepare a minor release with this. Should be easy.<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>On 24/7/21 13:45, Dmitry A. Semchonok wrote:<o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px'><div><p class=MsoNormal>Dear colleagues,<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Is there an official fix released already for the renaming the destination where original files are located?<o:p></o:p></p></div><div><p class=MsoNormal>I plan to do the Bayesian polishing but my original files have different location then previously.<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Thank you<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Sincerely,<o:p></o:p></p></div><div><p class=MsoNormal>Dmitry<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br><br><br><o:p></o:p></span></p><pre>_______________________________________________</pre><pre>scipion-users mailing list</pre><pre><a href="mailto:sci...@li...">sci...@li...</a></pre><pre><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre></blockquote><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>--<span class=apple-converted-space> </span><br>Pablo Conesa -<span class=apple-converted-space> </span><strong><span style='font-family:"Helvetica",sans-serif'>Madrid</span></strong><span class=apple-converted-space><b> </b></span><strong><span style='font-family:"Helvetica",sans-serif'><a href="http://scipion.i2pc.es/">Scipion</a></span></strong><span class=apple-converted-space><b> </b></span><strong><span style='font-family:"Helvetica",sans-serif'>team</span></strong><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>_______________________________________________<br>scipion-users mailing list<br></span><a href="mailto:sci...@li..."><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>sci...@li...</span></a><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br></span><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>https://lists.sourceforge.net/lists/listinfo/scipion-users</span></a><o:p></o:p></p></div></blockquote></div></div><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
|
From: Pablo C. <pc...@cn...> - 2021-07-27 12:20:44
|
Actually it seems we did it and forgot completely: scipion3 python -m pyworkflow.project.scripts.fix_links <project-name> <path_with_movies> Note, this will fix only movies import, other kind of imports is not yet available. On 27/7/21 9:31, Pablo Conesa wrote: > > Dear Dmitry, let me clarify that in this case is not a fix but a > feature: If you've moved the movies, paths are broken, and therefore, > bugs happens. > > I think we planned to release something like: "scipion3 fixlinks ..." > but is not done. > > > If you still need this, let me know we can prepare a minor release > with this. Should be easy. > > > On 24/7/21 13:45, Dmitry A. Semchonok wrote: >> >> Dear colleagues, >> >> Is there an official fix released already for the renaming the >> destination where original files are located? >> >> I plan to do the Bayesian polishing but my original files have >> different location then previously. >> >> Thank you >> >> Sincerely, >> >> Dmitry >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Pablo C. <pc...@cn...> - 2021-07-27 07:32:00
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Dear Dmitry, let me clarify that in this case is not a fix but a feature: If you've moved the movies, paths are broken, and therefore, bugs happens. I think we planned to release something like: "scipion3 fixlinks ..." but is not done. If you still need this, let me know we can prepare a minor release with this. Should be easy. On 24/7/21 13:45, Dmitry A. Semchonok wrote: > > Dear colleagues, > > Is there an official fix released already for the renaming the > destination where original files are located? > > I plan to do the Bayesian polishing but my original files have > different location then previously. > > Thank you > > Sincerely, > > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry A. S. <sem...@gm...> - 2021-07-26 19:56:36
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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;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .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>Issue with Bayesian polishing.<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 error says that the metadata was not found, my understanding is that original files are not on the place but currently this is not the case.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Would you please prompt what can case the issue?<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><o:p> </o:p></p><p class=MsoNormal><span style='color:#0070C0'>Hostname: cryoem01<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>PID: 37775<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>pyworkflow: 3.0.16<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>plugin: relion<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>plugin v: 3.1.2<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>currentDir: /data1/ScipionUserData/projects/20201211_apof_ph5_pos4<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>workingDir: Runs/009050_ProtRelionBayesianPolishing<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>runMode: Continue<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> MPI: 1<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> threads: 1<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> Starting at step: 1<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> Running steps <o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[35mSTARTED[0m: convertInputStep, step 1, time 2021-07-26 21:49:10.454974<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>Converting set from 'Runs/008377_ProtCryoSparcNewNonUniformRefine3D/particles.sqlite' into 'Runs/009050_ProtRelionBayesianPolishing/input_particles.star'<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>convertBinaryFiles: creating soft links.<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> Root: Runs/009050_ProtRelionBayesianPolishing/input/particles/input -> Runs/000427_ProtRelionExtractParticles/extra<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[35mFINISHED[0m: convertInputStep, step 1, time 2021-07-26 21:49:56.565214<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[35mSTARTED[0m: trainOrPolishStep, step 2, time 2021-07-26 21:49:56.684070<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[32m relion_motion_refine --i Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o Runs/009050_ProtRelionBayesianPolishing/extra --f Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac 0.500 --params3 --j 1 [0m<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> + Reading Runs/009050_ProtRelionBayesianPolishing/input_particles.star...<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>in: /opt/Scipion3/software/em/relion-3.1.2/src/jaz/micrograph_handler.cpp, line 264<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>ERROR: <o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>There is no movie metadata STAR file for any micrographs!<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>=== Backtrace ===<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x47e9d1]<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>relion_motion_refine(_ZN17MicrographHandler11loadInitialERKSt6vectorI13MetaDataTableSaIS1_EEbRiRdRSs+0xa60) [0x582890]<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>relion_motion_refine(_ZN17MicrographHandler4initERKSt6vectorI13MetaDataTableSaIS1_EEbiRiRdRSs+0x78) [0x585fc8]<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>relion_motion_refine(_ZN13MotionRefiner4initEv+0x516) [0x5077d6]<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>relion_motion_refine(main+0x31) [0x440391]<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f653431f555]<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>relion_motion_refine() [0x444570]<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>==================<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>ERROR: <o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>There is no movie metadata STAR file for any micrographs!<o:p></o:p></span></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 "/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 style='color:#0070C0'> self._run()<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> 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 style='color:#0070C0'> resultFiles = self._runFunc()<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> 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 style='color:#0070C0'> return self._func(*self._args)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 351, in trainOrPolishStep<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> self.runJob(self._getProgram('relion_motion_refine'), args)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1389, in runJob<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> process.runJob(log, programName, params,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> 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 style='color:#0070C0'> return runCommand(command, env, cwd)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> 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 style='color:#0070C0'> check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> 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 style='color:#0070C0'> raise CalledProcessError(retcode, cmd)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>subprocess.CalledProcessError: Command ' relion_motion_refine --i Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o Runs/009050_ProtRelionBayesianPolishing/extra --f Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac 0.500 --params3 --j 1 ' returned non-zero exit status 1.<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[31mProtocol failed: Command ' relion_motion_refine --i Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o Runs/009050_ProtRelionBayesianPolishing/extra --f Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac 0.500 --params3 --j 1 ' returned non-zero exit status 1.[0m<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[35mFAILED[0m: trainOrPolishStep, step 2, time 2021-07-26 21:50:07.277034<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>*** Last status is failed <o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[32m------------------- PROTOCOL FAILED (DONE 2/2)[0m<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><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Dmitry A. S. <sem...@gm...> - 2021-07-24 15:05:11
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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 colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Is there an official fix released already for the renaming the destination where original files are located?</p><p class=MsoNormal>I plan to do the Bayesian polishing but my original files have different location then previously.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you</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></div></body></html> |
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From: Dmitry S. <Sem...@gm...> - 2021-07-14 12:22:27
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Yes, I did and the problem persists. Sincerely, Dmitry > On 14. Jul 2021, at 13:53, Grigory Sharov <sha...@gm...> wrote: > > Have you tried to re-run this movie again with "Current relion MotionCorr" to reproduce bad output? > > If you can reproduce it, you could open an issue in relion repository specifying all necessary information for both cases. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Wed, Jul 14, 2021 at 12:37 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > Dear Grigory, > > So > > I check for example the 1 image that looks bad in current relion-motioncor protocol > But the same image was processed good in the older relion-motioncor protocol > > > > So what I did I took this image and processed it with MotionCorr protocol and everything worked just fine. > From left to right > > > Old relion MotionCorr > Current relion MotionCorr > Current MotionCorr > > > Hmm…. > > > > Any options? > > Thank you > > Sincerely, > Dmitry > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-07-14 11:54:04
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Have you tried to re-run this movie again with "Current relion MotionCorr" to reproduce bad output? If you can reproduce it, you could open an issue in relion repository specifying all necessary information for both cases. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Jul 14, 2021 at 12:37 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory, > > So > > I check for example the 1 image that looks bad in current relion-motioncor > protocol > But the same image was processed good in the older relion-motioncor > protocol > > > > So what I did I took this image and processed it with MotionCorr protocol > and everything worked just fine. > From left to right > > > Old relion MotionCorr > Current relion MotionCorr > Current MotionCorr > > > Hmm…. > > > > Any options? > > Thank you > > Sincerely, > Dmitry > > > > > > |
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From: Grigory S. <sha...@gm...> - 2021-07-14 10:04:01
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Please check first if the input movies and aligned mics are okay for black particles. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Jul 14, 2021 at 11:00 AM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory, > > > > You say > > I don't see any difference between the two screenshots. > > *The difference is the presence of trumbnail of movie + psd on old result > and absence on new (may be due to the version difference?)* > > > > > > Let me explain the all problem. > > > > I am currently try to find the reason why I have the error during 3D > refinement in both relion & cryosparc. > > > Bayesian polishing: > > During that step I received the first warning — the outcome images were > containing the black squares sometimes > > > > > > > > Then I tracked to relion - motion correction where I noticed that the > previous run with relion - motion correction (on the same dataset) have a > trumbnail of movie + psd > > Then I decided to do the CTF estimation (with gctf as previously) on the > suspicious relion- motion correction result and the outcome was wrong as > well. > Previously the output was fine > > (The images are identical — the differences may be in the version of > relion-motion cor!) > > > > > > > This one are the old results > > > > > > > So what do you thing may cause the error in the refinement/polishing-? > > > Thank you > > > Sincerely, > Dmitry > > > > > > > On 14. Jul 2021, at 11:12, Grigory Sharov <sha...@gm...> > wrote: > > HI don't see any difference between the two screenshots.. The first movie > is taken on carbon, so shifts are much smaller (look at the axes) compared > to the second "normal" movie in ice. > > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2021-07-14 09:31:43
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Dear Grigory, You say > I don't see any difference between the two screenshots. The difference is the presence of trumbnail of movie + psd on old result and absence on new (may be due to the version difference?) Let me explain the all problem. I am currently try to find the reason why I have the error during 3D refinement in both relion & cryosparc. Bayesian polishing: During that step I received the first warning — the outcome images were containing the black squares sometimes Then I tracked to relion - motion correction where I noticed that the previous run with relion - motion correction (on the same dataset) have a trumbnail of movie + psd Then I decided to do the CTF estimation (with gctf as previously) on the suspicious relion- motion correction result and the outcome was wrong as well. Previously the output was fine (The images are identical — the differences may be in the version of relion-motion cor!) This one are the old results So what do you thing may cause the error in the refinement/polishing-? Thank you Sincerely, Dmitry > On 14. Jul 2021, at 11:12, Grigory Sharov <sha...@gm...> wrote: > > HI don't see any difference between the two screenshots.. The first movie is taken on carbon, so shifts are much smaller (look at the axes) compared to the second "normal" movie in ice. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...>_______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-07-14 09:12:40
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Hello Dmitry, I don't see any difference between the two screenshots. The first movie is taken on carbon, so shifts are much smaller (look at the axes) compared to the second "normal" movie in ice. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... |
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From: Dmitry S. <Sem...@gm...> - 2021-07-14 08:59:47
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Dear colleagues, I have some suspicions about the correctness of the outcome I get from the relion motion correction protocol. Previously I received this output And now this one So any clue if the second outcome option is correct? Thank you Sincerely, Dmitry |
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From: David M. B. <Dav...@ut...> - 2021-07-12 19:02:28
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Dmitry, Handedness information is lost in 2D projection images. Therefore, when a 3D reconstruction is computed, the choice of hand is arbitrary. You simply need to flip the handedness to the correct one. Resolution will not change, only if you had some particles that were assigned a different handedness than other particles. But, that would not be a function of whether your starting reference had the correct handedness or not. It would be a function of whether the resolution range of your orientation alignment was appropriate. For example, at very low resolutions, handedness cannot be distinguished. At the high resolutions of many of today’s 3D reconstructions, one can set handedness by looking at the hand of alpha-helices or even individual amino acids if the resolution is high enough. Handedness also can be determined by doing a tilting experiment. Here are a couple older articles about tilt experiments that might be helpful: https://pubmed.ncbi.nlm.nih.gov/9356290/ https://pubmed.ncbi.nlm.nih.gov/14568533/ David From: "Dmitry A. Semchonok" <sem...@gm...> Reply-To: Mailing list for Scipion users <sci...@li...> Date: Monday, July 12, 2021 at 4:13 AM To: "sci...@li..." <sci...@li...> Subject: [scipion-users] refinement with unflipped reference Dear colleagues, Small theoretical question. After the 3D refinement it is appeared that the reference needed to be flipped. Do I need to redo the refinement with flipped reference? In general, do the processing with wrong hand reference decrease the resolution or the result is just the same? And why? Thank you Sincerely, Dmitry |
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From: Dmitry A. S. <sem...@gm...> - 2021-07-12 10:13:27
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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><div><p class=MsoNormal>Dear colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Small theoretical question.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>After the 3D refinement it is appeared that the reference needed to be flipped.</p><p class=MsoNormal>Do I need to redo the refinement with flipped reference? </p><p class=MsoNormal>In general, do the processing with wrong hand reference decrease the resolution or the result is just the same?</p><p class=MsoNormal>And why?</p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you</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></div></body></html> |
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