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Re: [scipion-users] deep consensus pickling error
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From: Carlos O. S. <co...@cn...> - 2021-04-19 10:56:53
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Dear Dmitry, let us see if David or Rubén knows where this environment is coming from. Kind regards, Carlos Oscar El 19/04/2021 a las 9:37, Pablo Conesa escribió: > > Hi Dmitry... you have no environment for xmipp_DLTK_v0.3. > > You have a "weird" xmipp_DLTK_v0.3_BACKUP2 > /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 > > > On 17/4/21 8:56, Dmitry A. Semchonok wrote: >> >> Dear colleagues, >> >> During deep consensus pickling I received the following error >> >> Any ideas? >> >> Thank you >> >> Sincerely, >> >> Dmitry >> >> [Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min >> >> [Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min >> >> [Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min >> >> [Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min >> >> [Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min >> >> [Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min >> >> [Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min >> >> [Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min >> >> [Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min >> >> [Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished >> >> [35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 >> 04:05:07.093613 >> >> [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 >> 04:05:07.574152 >> >> [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 >> 04:26:59.879548 >> >> [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444 >> >> None None None None >> >> $ /usr/local/EMAN_2.21/bin/conda info --env >> >> # conda environments: >> >> # >> >> 3DFSC /home/panos/.conda/envs/3DFSC >> >> cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 >> >> cryolo /home/panos/.conda/envs/cryolo >> >> xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 >> >> cryolo /usr/local/EMAN_2.21/envs/cryolo >> >> cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4 >> >> fsc /usr/local/EMAN_2.21/envs/fsc >> >> topaz /usr/local/EMAN_2.21/envs/topaz >> >> root * /usr/local/EMAN_2.21 >> >> >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above) >> >> Traceback (most recent call last): >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", >> line 189, in run >> >> self._run() >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", >> line 240, in _run >> >> resultFiles = self._runFunc() >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", >> line 236, in _runFunc >> >> return self._func(*self._args) >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deepConsensus.py", >> line 948, in trainCNN >> >> env=self.getCondaEnv()) >> >> File >> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", >> line 204, in getCondaEnv >> >> return CondaEnvManager.getCondaEnv(env, envName) >> >> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in >> getCondaEnv >> >> envBin = os.path.join(environDir, "bin") >> >> File "/usr/lib64/python3.6/posixpath.py", line 80, in join >> >> a = os.fspath(a) >> >> TypeError: expected str, bytes or os.PathLike object, not NoneType >> >> [31mProtocol failed: expected str, bytes or os.PathLike object, not >> NoneType[0m >> >> [35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417 >> >> *** Last status is failed >> >> 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 > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
