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Re: [scipion-users] Cryosparc 2D - Scipion issue
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From: Pablo C. <pc...@cn...> - 2021-08-31 14:15:19
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I posted a possible solution there: "Have you got software/em/pyem-0.4 folder. If so, try to remove it and then run scipion3 installb pyem" On 31/8/21 13:40, Jose Miguel de la Rosa Trevin wrote: > I had a similar issue than Dmitry....at some point the same error that > here...but then another one. Reported last Friday here: > > https://github.com/scipion-em/scipion-em-cryosparc2/issues/91 > <https://github.com/scipion-em/scipion-em-cryosparc2/issues/91> > > > > > > On Tue, Aug 31, 2021 at 11:29 AM Pablo Conesa <pc...@cn... > <mailto:pc...@cn...>> wrote: > > Hi! > > It seems there is a mismatch of versions. Could you please send > the output of: > > > scipion3 run pip list > > > And the output of: > > ls -l <SCIPION_HOME>/software/em | grep pyem > > > On 25/8/21 8:07, pc...@cn... <mailto:pc...@cn...> > wrote: >> Hi Dmitry, give us some time. Probably until next week to >> investigate. >> >> El 23 ago. 2021 22:22, "Dmitry A. Semchonok" >> <sem...@gm...> <mailto:sem...@gm...> escribió: >> >> >> Dear colleagues, >> >> After the installation of the latest modules for the >> cryosparc//relion the 2D classification in SCIPION3 is >> finishing with the error, although in cryosparc itself the 2D >> classification finished correctly. >> >> Could you please advice how to fix that? >> >> Thank you >> >> Sincerely, >> >> Dmitry >> >> Creating the output... >> >> 00032: Traceback (most recent call last): >> >> 00033: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 197, in run >> >> 00034: self._run() >> >> 00035: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 248, in _run >> >> 00036: resultFiles = self._runFunc() >> >> 00037: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 244, in _runFunc >> >> 00038: return self._func(*self._args) >> >> 00039: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", >> line 282, in createOutputStep >> >> 00040: convertCs2Star(args) >> >> 00041: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", >> line 99, in convertCs2Star >> >> 00042: df = star.remove_deprecated_relion2(df, >> inplace=True) >> >> 00043: AttributeError: module 'pyem.star' has no attribute >> 'remove_deprecated_relion2' >> >> 00044: Protocol failed: module 'pyem.star' has no attribute >> 'remove_deprecated_relion2' >> >> 00045: FAILED: createOutputStep, step 3, time 2021-08-22 >> 13:57:23.830243 <tel:23.830243> >> >> 00046: *** Last status is failed >> >> 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN >> is set to True. >> >> 00048: ------------------- PROTOCOL FAILED (DONE 3/3) >> >> >> >> Hi Dmitry, give us some time. Probably until next week to investigate. >> >> >> El 23 ago. 2021 22:22, "Dmitry A. Semchonok"<sem...@gm...> <mailto:sem...@gm...> escribió: >>> Dear colleagues, >>> >>> >>> >>> After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly. >>> >>> >>> >>> Could you please advice how to fix that? >>> >>> >>> >>> >>> >>> Thank you >>> >>> >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> >>> >>> >>> >>> >>> Creating the output... >>> >>> 00032: Traceback (most recent call last): >>> >>> 00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run >>> >>> 00034: self._run() >>> >>> 00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run >>> >>> 00036: resultFiles = self._runFunc() >>> >>> 00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc >>> >>> 00038: return self._func(*self._args) >>> >>> 00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep >>> >>> 00040: convertCs2Star(args) >>> >>> 00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star >>> >>> 00042: df = star.remove_deprecated_relion2(df, inplace=True) >>> >>> 00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2' >>> >>> 00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' >>> >>> 00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:23.830243 >>> >>> 00046: *** Last status is failed >>> >>> 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True. >>> >>> 00048: ------------------- PROTOCOL FAILED (DONE 3/3) >>> >>> >>> >>> > -- > 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> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
