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Re: [scipion-users] SCIPION__3___installing plugins/protocols
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From: Dmitry A. S. <sem...@gm...> - 2020-11-20 17:42:16
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Please see below
[32mRUNNING PROTOCOL -----------------[0m
Hostname: cryoem01
PID: 6073
pyworkflow: 3.0.7
plugin: motioncorr
plugin v: 3.0.11
currentDir: /root/ScipionUserData/projects/TestMotioncor2AlignMovies
workingDir: Runs/000410_ProtMotionCorr
runMode: Continue
MPI: 1
threads: 1
Starting at step: 1
Running steps
[35mSTARTED[0m: _convertInputStep, step 1, time 2020-11-20 18:14:46.299801
[35mFINISHED[0m: _convertInputStep, step 1, time 2020-11-20 18:14:46.308113
[35mSTARTED[0m: processMovieStep, step 2, time 2020-11-20 18:14:46.323599
Processing movie: Runs/000410_ProtMotionCorr/tmp/movie_000001/qbeta.mrc
[32m/opt/Scipion3/software/em/motioncor2-1.3.2/bin/MotionCor2_1.3.2-Cuda101 -InMrc "qbeta.mrc" -OutMrc "../../extra/qbeta_aligned_mic.mrc" -Patch 2 2 -MaskCent 0 0 -MaskSize 1 1 -FtBin 1.0 -Tol 0.5 -Group 1 -FmDose 1.3 -Throw 1 -Trunc 1 -PixSize 1.0 -kV 300.0 -LogFile ../../extra/micrograph_000001_ -InitDose 0.0 -OutStack 0 -Gpu 0 -SumRange 0.0 0.0 [0m
/opt/Scipion3/software/em/motioncor2-1.3.2/bin/MotionCor2_1.3.2-Cuda101: error while loading shared libraries: libcudart.so.10.1: cannot open shared object file: No such file or directory
ERROR: Movie failed
[35mFINISHED[0m: processMovieStep, step 2, time 2020-11-20 18:14:46.350371
[31mERROR: Movie Runs/000002_ProtImportMovies/extra/qbeta.mrc couldn't be added to the output set.
[Errno 2] No such file or directory: 'Runs/000410_ProtMotionCorr/extra/micrograph_000001_0-Patch-Full.log'[0m
[33mWARNING: Micrograph Runs/000410_ProtMotionCorr/extra/qbeta_aligned_mic.mrc was not generated, can't add it to output set.[0m
[33mWARNING: Micrograph Runs/000410_ProtMotionCorr/extra/qbeta_aligned_mic_DW.mrc was not generated, can't add it to output set.[0m
[35mSTARTED[0m: createOutputStep, step 3, time 2020-11-20 18:14:49.416644
Traceback (most recent call last):
File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 187, in run
self._run()
File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run
resultFiles = self._runFunc()
File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc
return self._func(*self._args)
File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pwem/protocols/protocol_align_movies.py", line 120, in createOutputStep
raise Exception("All movies failed, didn't create outputMicrographs."
Exception: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.
[31mProtocol failed: All movies failed, didn't create outputMicrographs.Please review movie processing steps above.[0m
[35mFAILED[0m: createOutputStep, step 3, time 2020-11-20 18:14:49.424758
[32m------------------- PROTOCOL FAILED (DONE 3/3)[0m
Sincerely,
Dmitry
On November 20, 2020 2:54:01 PM Grigory Sharov <sha...@gm...> wrote:
> 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 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
>
> On Fri, Nov 20, 2020 at 1:41 PM Dmitry Semchonok <Sem...@gm... <mailto: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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