Re: [scipion-users] Cryosparc 2D - Scipion issue

[Jose M. de la R. T. <del...@gm...>]

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





On Tue, Aug 31, 2021 at 11:29 AM Pablo Conesa <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... wrote:
>
> Hi Dmitry, give us some time. Probably until next week to investigate.
>
> El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <sem...@gm...>
> <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)
>
>
>
>
>
>
>
> Hi Dmitry, give us some time. Probably until next week to investigate.
>
>
> El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <sem...@gm...> <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*
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