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[scipion-users] deep consensus pickling error
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From: Dmitry A. S. <sem...@gm...> - 2021-04-17 06:56:31
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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 colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>During deep consensus pickling I received the following error</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Any ideas?</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><o:p> </o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min</p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished</p><p class=MsoNormal>[35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 04:05:07.093613</p><p class=MsoNormal>[35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:05:07.574152</p><p class=MsoNormal>[35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:26:59.879548</p><p class=MsoNormal>[35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444</p><p class=MsoNormal>None None None None</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>$ /usr/local/EMAN_2.21/bin/conda info --env</p><p class=MsoNormal># conda environments:</p><p class=MsoNormal>#</p><p class=MsoNormal>3DFSC /home/panos/.conda/envs/3DFSC</p><p class=MsoNormal>cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0</p><p class=MsoNormal>cryolo /home/panos/.conda/envs/cryolo</p><p class=MsoNormal>xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2</p><p class=MsoNormal>cryolo /usr/local/EMAN_2.21/envs/cryolo</p><p class=MsoNormal>cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4</p><p class=MsoNormal>fsc /usr/local/EMAN_2.21/envs/fsc</p><p class=MsoNormal>topaz /usr/local/EMAN_2.21/envs/topaz</p><p class=MsoNormal>root * /usr/local/EMAN_2.21</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)</p><p class=MsoNormal>Traceback (most recent call last):</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run</p><p class=MsoNormal> self._run()</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run</p><p class=MsoNormal> resultFiles = self._runFunc()</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc</p><p class=MsoNormal> return self._func(*self._args)</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deepConsensus.py", line 948, in trainCNN</p><p class=MsoNormal> env=self.getCondaEnv())</p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv</p><p class=MsoNormal> return CondaEnvManager.getCondaEnv(env, envName)</p><p class=MsoNormal> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv</p><p class=MsoNormal> envBin = os.path.join(environDir, "bin")</p><p class=MsoNormal> File "/usr/lib64/python3.6/posixpath.py", line 80, in join</p><p class=MsoNormal> a = os.fspath(a)</p><p class=MsoNormal>TypeError: expected str, bytes or os.PathLike object, not NoneType</p><p class=MsoNormal>[31mProtocol failed: expected str, bytes or os.PathLike object, not NoneType[0m</p><p class=MsoNormal>[35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417</p><p class=MsoNormal>*** Last status is failed</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> |
