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Re: [scipion-users] relion 3D auto refinement error (after Bayesian polishing)
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From: Dmitry A. S. <sem...@gm...> - 2021-07-11 13:30:32
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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>Dear Grigory & all,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I tried 3D auto refinement with no mask – the same result – error</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>But when I changed the reference – I was able to start the process!</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><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 style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:sha...@gm...">Grigory Sharov</a><br><b>Sent: </b>Sunday, July 11, 2021 2:48 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] relion 3D auto refinement error (after Bayesian polishing)</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi,</p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I haven't seen such an error before but I would guess your input mask file is corrupted.<br clear=all></p><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>Best regards,<br>Grigory</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>--------------------------------------------------------------------------------</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>Grigory Sharov, Ph.D.<br><br>MRC Laboratory of Molecular Biology,<br>Francis Crick Avenue,<br>Cambridge Biomedical Campus,<br>Cambridge CB2 0QH, UK.<br>tel. </span><span style='color:black'><a href="tel:+44%201223%20267228" target="_blank"><span style='font-size:9.5pt;color:#1155CC'>+44 (0) 1223 267228</span></a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>e-mail: </span><span style='color:black'><a href="mailto:gs...@mr..." target="_blank"><span style='font-size:9.5pt;color:#1155CC'>gs...@mr...</span></a><o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Sat, Jul 10, 2021 at 7:58 PM Dmitry A. Semchonok <<a href="mailto:sem...@gm...">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>Thank you Grigory,</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>But now the next error -</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>RUNNING PROTOCOL -----------------</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00002: Hostname: localhost4.localdomain4</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00003: PID: 108841</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00004: pyworkflow: 3.0.16</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00005: plugin: relion</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00006: plugin v: 3.1.2</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00007: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00008: workingDir: Runs/065340_ProtRelionRefine3D</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00009: runMode: Restart</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00010: MPI: 7</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00011: threads: 6</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00012: relion_image_handler: /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so.5: no version information available (required by relion_image_handler)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00013: 000/??? sec ~~(,_,"> [oo]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00014: 3/ 3 sec ..........................................................~~(,_,"></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00015: ** 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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00016: Starting at step: 1</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00017: Running steps </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00018: STARTED: convertInputStep, step 1, time 2021-07-10 20:53:24.092629</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00019: Converting set from 'Runs/065197_ProtUserSubSet/particles.sqlite' into 'Runs/065340_ProtRelionRefine3D/input_particles.star'</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00020: relion_image_handler: /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so.5: no version information available (required by relion_image_handler)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00021: 000/??? sec ~~(,_,"> [oo]in: /home/user/Data/Software/scipion3/software/em/relion-3.1.2/src/multidim_array.h, line 678</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00022: ERROR: </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00023: coreAllocate:Cannot allocate a negative number of bytes</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00024: === Backtrace ===</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00025: relion_image_handler(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x4bc051]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00026: relion_image_handler(_ZN13MultidimArrayI8tComplexIdEE12coreAllocateEv+0x25e) [0x44826e]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00027: relion_image_handler(_ZN13MultidimArrayI8tComplexIdEE9initZerosEllll+0x168) [0x4b2818]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00028: relion_image_handler(_Z22windowFourierTransformI8tComplexIdEEvR13MultidimArrayIT_ES5_l+0x75) [0x4b2965]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00029: relion_image_handler(_Z9resizeMapR13MultidimArrayIdEi+0x378) [0x4acfc8]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00030: relion_image_handler(_ZN24image_handler_parameters18perImageOperationsER5ImageIdER8FileNamed+0x969) [0x457eb9]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00031: relion_image_handler(_ZN24image_handler_parameters3runEv+0x2363) [0x45d403]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00032: relion_image_handler(main+0x31) [0x4392e1]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00033: /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f1a1750d555]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00034: relion_image_handler() [0x43cf9f]</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00035: ==================</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00036: ERROR: </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00037: coreAllocate:Cannot allocate a negative number of bytes</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00038: convertBinaryFiles: creating soft links.</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00039: Root: Runs/065340_ProtRelionRefine3D/extra/input -> Runs/064819_ProtRelionBayesianPolishing/extra</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00040: ** Running command: relion_image_handler --i Runs/065419_ProtImportVolumes/extra/import_cryosparc_P12_J26_008_volume_map.mrc --o Runs/065340_ProtRelionRefine3D/tmp/import_cryosparc_P12_J26_008_volume_map.00.mrc --angpix 9612.00000 --rescale_angpix 0.96120 --new_box 384</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00041: Traceback (most recent call last):</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00042: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00043: self._run()</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00044: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00045: resultFiles = self._runFunc()</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00046: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00047: return self._func(*self._args)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00048: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 803, in convertInputStep</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00049: self._convertRef()</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00050: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 1249, in _convertRef</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00051: self._convertVol(refVols[0])</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00052: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 1232, in _convertVol</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00053: relion.convert.convertMask(inputVol, outputFn, newPix=newPix,</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00054: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/convert_utils.py", line 224, in convertMask</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00055: pwutils.runJob(None, 'relion_image_handler', params, env=Plugin.getEnviron())</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00056: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00057: return runCommand(command, env, cwd)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00058: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00059: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00060: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00061: raise CalledProcessError(retcode, cmd)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00062: subprocess.CalledProcessError: Command ' relion_image_handler --i Runs/065419_ProtImportVolumes/extra/import_cryosparc_P12_J26_008_volume_map.mrc --o Runs/065340_ProtRelionRefine3D/tmp/import_cryosparc_P12_J26_008_volume_map.00.mrc --angpix 9612.00000 --rescale_angpix 0.96120 --new_box 384' returned non-zero exit status 1.</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00063</span><span lang=EN-GB style='color:red'>: Protocol failed: Command ' relion_image_handler --i Runs/065419_ProtImportVolumes/extra/import_cryosparc_P12_J26_008_volume_map.mrc --o Runs/065340_ProtRelionRefine3D/tmp/import_cryosparc_P12_J26_008_volume_map.00.mrc --angpix 9612.00000 --rescale_angpix 0.96120 --new_box 384' returned non-zero exit status 1.</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00064: FAILED: convertInputStep, step 1, time 2021-07-10 20:53:37.235999</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00065: *** Last status is failed </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB style='color:#0070C0'>00066: ------------------- PROTOCOL FAILED (DONE 1/3)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b>From: </b><a href="mailto:sha...@gm..." target="_blank">Grigory Sharov</a><br><b>Sent: </b>Saturday, July 10, 2021 5:14 PM<br><b>To: </b><a href="mailto:sci...@li..." target="_blank">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] relion 3D auto refinement error (after Bayesian polishing)</p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi Dmitry,</p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>This one is easy. You need to remove brackets from the file name <span style='font-size:9.5pt;font-family:"Arial",sans-serif;color:#0070C0'>Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc before import</span></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Sat, Jul 10, 2021, 15:47 Dmitry A. Semchonok <<a href="mailto:sem...@gm..." target="_blank">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear Grigory & colleagues,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>During relion 3D refinement I received the error – please see below.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Prehistory – I run the Bayesian polishing with the relion 3D refinement dataset (<span style='color:#0070C0'>syntax error near unexpected token `('</span>).</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I suspect there are some errors in Bayesian polishing outcome dataset. Some of them I fixed by deleting black images.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>So the question is how to fix the remaining errors to let the relion 3D refinement run?</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thank you in advance,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sincerely,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dmitry</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>RUNNING PROTOCOL -----------------</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00002: Hostname: localhost4.localdomain4</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00003: PID: 86173</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00004: pyworkflow: 3.0.16</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00005: plugin: relion</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00006: plugin v: 3.1.2</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00007: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00008: workingDir: Runs/065340_ProtRelionRefine3D</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00009: runMode: Continue</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00010: MPI: 7</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00011: threads: 6</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00012: /bin/sh: -c: line 0: syntax error near unexpected token `('</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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'</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00015: Traceback (most recent call last):</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00017: self._run()</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00019: self._insertAllSteps() # Define steps for execute later</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00021: self._insertRelionStep()</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00023: self._setNormalArgs(args)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00025: self._setBasicArgs(args)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00027: self._setMaskArgs(args)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00029: mask = relion.convert.convertMask(self.referenceMask.get(),</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00031: pwutils.runJob(None, 'relion_image_handler', params, env=Plugin.getEnviron())</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00033: return runCommand(command, env, cwd)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00035: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00036: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00037: raise CalledProcessError(retcode, cmd)</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'>00039: ------------------- PROTOCOL FAILED (DONE 0/0) </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#0070C0'> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div></blockquote></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:4.8pt'>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div></blockquote></div><p class=MsoNormal style='margin-left:4.8pt'>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
