[scipion-users] movie alignment protocols error

[Dmitry S. <sem...@gm...>]

Dear colleagues,


The issue is  the following - none of the movie alignment protocols is
currently working fine at our cluster.


Please see the errors below:



*The xmipp3 – movie alignment (xmipp3-optical alignment) (run on GPU)*

2017-04-11 10:56:49.125723

00080:   Traceback (most recent call last):

00081:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 184, in run

00082:       self._run()

00083:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 1034, in _run

00084:       self._runSteps(startIndex)

00085:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 919, in _runSteps

00086:       self._stepsCheck)

00087:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/executor.py",
line 119, in runSteps

00088:       stepsCheckCallback()

00089:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_movies.py",
line 150, in _stepsCheck

00090:       self._checkNewOutput()

00091:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_align_movies.py",
line 222, in _checkNewOutput

00092:       'outputMicrographs')

00093:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_align_movies.py",
line 193, in _updateOutputMicSet

00094:       micSet = self._loadOutputSet(SetOfMicrographs, sqliteFn)

00095:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_align_movies.py",
line 122, in _loadOutputSet

00096:       outputSet.loadAllProperties()

00097:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/object.py",
line 1196, in loadAllProperties

00098:       for key in self._getMapper().getPropertyKeys():

00099:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/mapper/sqlite.py",
line 920, in getPropertyKeys

00100:       return self.db.getPropertyKeys()

00101:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/mapper/sqlite.py",
line 1017, in getPropertyKeys

00102:       self.executeCommand(self.SELECT_PROPERTY_KEYS)

00103:   OperationalError: no such table: Properties

00104:   ------------------- PROTOCOL FAILED (DONE 2/5141)







*Motioncorr – motioncorr alignment (GPU)*

STARTED: processMovieStep, step 1

00012:     2017-04-11 10:44:05.586468

00013:   Processing movie:
Runs/021173_ProtMotionCorr/tmp/movie_000001/FoilHole_26594250_Data_25564800_25564801_20160826_2007-21923.mrc

00014:   Traceback (most recent call last):

00015:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 184, in run

00016:       self._run()

00017:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 230, in _run

00018:       resultFiles = self._runFunc()

00019:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 226, in _runFunc

00020:       return self._func(*self._args)

00021:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_movies.py",
line 267, in processMovieStep

00022:       self._processMovie(movie)

00023:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/packages/motioncorr/protocol_motioncorr.py",
line 304, in _processMovie

00024:       if self.doMagCor and self._supportsMagCorrection():

00025:   AttributeError: 'ProtMotionCorr' object has no attribute 'doMagCor'

00026:   Protocol failed: 'ProtMotionCorr' object has no attribute
'doMagCor'

00027:   FAILED: processMovieStep, step 1

00028:     2017-04-11 10:44:05.613162

00029:   ------------------- PROTOCOL FAILED (DONE 1/5141)



*Grigoriefflab-unblur*

00738:   Total execution time : 1 minute and 7 seconds

00739:   2017-04-11 13:20:05  : UnBlur finished cleanly.

00740:

00741:   Erasing.....movieFolder: Runs/022622_ProtUnblur/tmp/movie_000005

00742:   Traceback (most recent call last):

00743:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 184, in run

00744:       self._run()

00745:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 1034, in _run

00746:       self._runSteps(startIndex)

00747:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py",
line 919, in _runSteps

00748:       self._stepsCheck)

00749:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/executor.py",
line 220, in runSteps

00750:       stepsCheckCallback()

00751:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_movies.py",
line 150, in _stepsCheck

00752:       self._checkNewOutput()

00753:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_align_movies.py",
line 180, in _checkNewOutput

00754:       newMovie = self._createOutputMovie(movie)

00755:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_align_movies.py",
line 352, in _createOutputMovie

00756:       xshifts, yshifts = self._getMovieShifts(movie)

00757:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/packages/grigoriefflab/protocol_unblur.py",
line 316, in _getMovieShifts

00758:       xShifts, yShifts = readShiftsMovieAlignment(shiftFn)

00759:     File
"/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/packages/grigoriefflab/convert.py",
line 247, in readShiftsMovieAlignment

00760:       f = open(shiftFn)

00761:   IOError: [Errno 2] No such file or directory:
'Runs/022622_ProtUnblur/extra/FoilHole_26594250_Data_25564906_25564907_20160826_2009-21925_shifts.txt'

00762:   ------------------- PROTOCOL FAILED (DONE 1/5141)









*Xmipp3 – correlation alignment –(Threads)*

Was running till step 1075 then failed – I resubmitted it and again it
crashed after a few images.



00423:   2017-04-11 12:54:52,577 ERROR:  Protocol failed: (-10.0, 0.0,
u'\u221210', 'k', 'top', 'center', 7057509111269643423, None, None, 100,
140391271392104)

00424:   2017-04-11 12:54:52,639 INFO:  FAILED: processMovieStep, step 1075

00425:   2017-04-11 12:54:52,640 INFO:    2017-04-11 12:54:34.176712

00426:   2017-04-11 12:54:52,779 INFO:  ------------------- PROTOCOL FAILED
(DONE 1077/5141)

00427:   2017-04-11 12:55:08,985 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001097

00428:   2017-04-11 12:56:23,125 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001098

00429:   2017-04-11 12:56:36,576 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001099

00430:   2017-04-11 12:57:14,722 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001102

00431:   2017-04-11 12:57:18,171 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001101

00432:   2017-04-11 12:57:18,744 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001103

00433:   2017-04-11 12:57:21,819 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001100

00434:   2017-04-11 12:57:22,569 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001105

00435:   2017-04-11 12:57:30,870 INFO:  Erasing.....movieFolder:
Runs/022537_XmippProtMovieCorr/tmp/movie_001104

00436:   2017-04-11 12:57:31,472 INFO:  ------------------- PROTOCOL FAILED
(DONE 1077/5141)





Any ideas why?



Thank you.



Sincerely,

Dmitry