Re: [scipion-users] xmipp movie extract 'ProgrammingError' recursive use of commas not allowed

[David M. <dma...@cn...>]

This sounds like it's trying to read/write to .sqlite in threads and sqlite
doesn't support threating.

Therefore, try to run the protocol with *1 thread* and *1 MPI*.


Thanks for your comment!

<http://ucm.es/>

*_____Dr. David Maluenda Niubó*
dma...@cn... - (+34) 619 029 310
CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

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On Tue, Aug 7, 2018 at 2:49 PM Matthews-Palmer, Teige Rowan Seal <
t.m...@im...> wrote:

> Dear Scipion users,
>
> I am getting the following error in Caligula v1.2, from the protocol
> xmipp3 extract movie particles:
>
> Any ideas or help greatly appreciated.
> All the best,
>
> Teige
>
>
> 00086:   Traceback (most recent call last):
> 00087:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/executor.py",
> line 137, in run
> 00088:       self.step._run()  # not self.step.run() , to avoid race
> conditions
> 00089:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py",
> line 233, in _run
> 00090:       resultFiles = self._runFunc()
> 00091:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py",
> line 229, in _runFunc
> 00092:       return self._func(*self._args)
> 00093:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/protocol/protocol_movies.py",
> line 234, in processMovieStep
> 00094:       if self._filterMovie(movie):
> 00095:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/packages/xmipp3/protocol_extract_particles_movies.py",
> line 434, in _filterMovie
> 00096:       micrograph = micSet[movieId]
> 00097:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1040,
> in __getitem__
> 00098:       return self._getMapper().selectById(itemId)
> 00099:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1025,
> in _getMapper
> 00100:       self.load()
> 00101:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1117,
> in load
> 00102:       self._idCount = self._mapper.maxId()
> 00103:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line
> 900, in maxId
> 00104:       return 0 if self.doCreateTables else self.db.maxId()
>
>
> *00105:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line
> 1201, in maxId 00106:
> self.executeCommand(self.selectCmd('1').replace('*', 'MAX(id)')) 00107:
> ProgrammingError: Recursive use of cursors not allowed.*
>
>
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