Menu
▾
▴
[scipion-users] installation running issues
|
From: Dmitry A. S. <sem...@gm...> - 2020-05-27 14:13:03
|
Dear colleagues,
During the test of SCIPION on the new server we got the error on during
motion correction step (original files are in the attachment)
How to fix this issue?
Thank you!
Sincerely,
Dmitry
=========================================
run
2020-05-27 15:47:19,297 INFO: [35mSTARTED[0m: waitForThreadStep, step
12
2020-05-27 15:47:19,297 INFO: 2020-05-27 15:47:19.297160
2020-05-27 15:47:19,301 INFO: [35mFINISHED[0m: waitForThreadStep,
step 12
2020-05-27 15:47:19,301 INFO: 2020-05-27 15:47:19.299252
2020-05-27 15:47:19,302 INFO: [35mSTARTED[0m: createOutputStep, step
13
2020-05-27 15:47:19,302 INFO: 2020-05-27 15:47:19.302209
2020-05-27 15:47:19,305 ERROR: [31mProtocol failed: [31mAll movies
failed, didn't create outputMicrographs.Please review movie processing
steps above.[0m[0m
2020-05-27 15:47:19,308 INFO: [35mFAILED[0m: createOutputStep, step
13
2020-05-27 15:47:19,308 INFO: 2020-05-27 15:47:19.304107
2020-05-27 15:47:19,311 INFO: [32m------------------- PROTOCOL FAILED
(DONE 13/13)[0m
2020-05-27 15:47:19,321 INFO: [32m------------------- PROTOCOL FAILED
(DONE 13/13)[0m
==========================================
run.stdout
...... Frame ( 25) shift: 0.000 0.000
...... Frame ( 26) shift: 0.000 0.000
...... Frame ( 27) shift: 0.000 0.000
...... Frame ( 28) shift: 0.000 0.000
...... Frame ( 29) shift: 0.000 0.000
...... Frame ( 30) shift: 0.000 0.000
ERROR: Movie failed
[35mFINISHED[0m: processMovieStep, step 11
2020-05-27 15:47:19.274026
[33mWARNING: Movie
Runs/000002_ProtImportMovies/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions.mrc
has empty alignment data, can't add it to output set.[0m
[33mWARNING: Micrograph
Runs/000085_ProtMotionCorr/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions_aligned_mic.mrc
was not generated, can't add it to output set.[0m
[33mWARNING: Micrograph
Runs/000085_ProtMotionCorr/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions_aligned_mic_DW.mrc
was not generated, can't add it to output set.[0m
[35mSTARTED[0m: waitForThreadStep, step 12
2020-05-27 15:47:19.297160
[35mFINISHED[0m: waitForThreadStep, step 12
2020-05-27 15:47:19.299252
[35mSTARTED[0m: createOutputStep, step 13
2020-05-27 15:47:19.302209
Traceback (most recent call last):
File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, in
run
self._run()
File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, in
_run
resultFiles = self._runFunc()
File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, in
_runFunc
return self._func(*self._args)
File
"/usr/local/scipion/pyworkflow/em/protocol/protocol_align_movies.py",
line 117, in createOutputStep
raise Exception(redStr("All movies failed, didn't create
outputMicrographs."
Exception: [31mAll movies failed, didn't create
outputMicrographs.Please review movie processing steps above.[0m
[31mProtocol failed: [31mAll movies failed, didn't create
outputMicrographs.Please review movie processing steps above.[0m[0m
[35mFAILED[0m: createOutputStep, step 13
2020-05-27 15:47:19.304107
[32m------------------- PROTOCOL FAILED (DONE 13/13)[0m |
