Re: [scipion-users] deep consensus pickling error

[Pablo C. <pc...@cn...>]

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
>
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> Windows 10
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*