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

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

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...> 
> 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...> 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*