Re: [scipion-users] SCIPION__3___installing plugins/protocols

[Grigory S. <sha...@gm...>]

Dear Dmitry,

Could you please run *scipion tests
motioncorr.tests.test_protocols_motioncor2* and post the *run.stdout* here?



Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Fri, Nov 20, 2020 at 1:41 PM Dmitry Semchonok <Sem...@gm...>
wrote:

> Dear colleagues,
>
>  We have some issues during SCIPION3 plugins installations.
>
>  Any suggestions?
>
>  Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
>
>
> *Motion cor error:*
>
>
> 00279:   WARNING: Micrograph
> Runs/000174_ProtMotionCorr/extra/20170629_00049_frameImage_aligned_mic_DW.mrc
> was not generated, can't add it to output set.
>
> 00280:   STARTED: createOutputStep, step 26, time 2020-11-20
> 14:16:28.063854
>
> 00281:   Traceback (most recent call last):
>
> 00282:     File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 187, in run
>
> 00283:       self._run()
>
> 00284:     File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 238, in _run
>
> 00285:       resultFiles = self._runFunc()
>
> 00286:     File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 234, in _runFunc
>
> 00287:       return self._func(*self._args)
>
> 00288:     File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py",
> line 120, in createOutputStep
>
> 00289:       raise Exception("All movies failed, didn't create
> outputMicrographs."
>
> 00290:   Exception: All movies failed, didn't create
> outputMicrographs.Please review movie processing steps above.
>
> 00291:   Protocol failed: All movies failed, didn't create
> outputMicrographs. Please review movie processing steps above.
>
> 00292:   FAILED: createOutputStep, step 26, time 2020-11-20 14:16:28.070889
>
> 00293:   ------------------- PROTOCOL FAILED (DONE 26/26)
>
>
>
> *GCTF:*
>
>
>
> 00279:   WARNING: Micrograph
> Runs/000174_ProtMotionCorr/extra/20170629_00049_frameImage_aligned_mic_DW.mrc
> was not generated, can't add it to output set.
>
> 00280:   STARTED: createOutputStep, step 26, time 2020-11-20
> 14:16:28.063854
>
> 00281:   Traceback (most recent call last):
>
> 00282:     File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 187, in run
>
> 00283:       self._run()
>
> 00284:     File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 238, in _run
>
> 00285:       resultFiles = self._runFunc()
>
> 00286:     File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",
> line 234, in _runFunc
>
> 00287:       return self._func(*self._args)
>
> 00288:     File
> "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py",
> line 120, in createOutputStep
>
> 00289:       raise Exception("All movies failed, didn't create
> outputMicrographs."
>
> 00290:   Exception: All movies failed, didn't create
> outputMicrographs.Please review movie processing steps above.
>
> 00291:   Protocol failed: All movies failed, didn't create
> outputMicrographs.Please review movie processing steps above.
>
> 00292:   FAILED: createOutputStep, step 26, time 2020-11-20 14:16:28.070889
>
> 00293:   ------------------- PROTOCOL FAILED (DONE 26/26)
>
>
>
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