[scipion-users] shire cryolo picking error

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

Dear colleagues,


The shire cryolo picking ends up after few micrographs picking with the following error:



INISHED: pickMicrographListStep, step 9, time 2021-08-04 11:38:10.274708
00762:   Reading coordinates from mics: 81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128
00763:   Traceback (most recent call last):
00764:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/convert.py", line 100, in iterCoords
00765:       if self._getDataLength() == 7:  # crYOLO generates .cbox files with 7 columns from version > 1.5.4
00766:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/convert.py", line 92, in _getDataLength
00767:       head = next(self._file)  # Read the first line
00768:   StopIteration
00769:   
00770:   The above exception was the direct cause of the following exception:
00771:   
00772:   Traceback (most recent call last):
00773:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run
00774:       self._run()
00775:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1367, in _run
00776:       self._runSteps(startIndex)
00777:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1218, in _runSteps
00778:       self._stepsExecutor.runSteps(self._steps,
00779:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 131, in runSteps
00780:       stepsCheckCallback()
00781:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 301, in _stepsCheck
00782:       self._checkNewOutput()
00783:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 400, in _checkNewOutput
00784:       newDoneUpdated = self._updateOutputCoordSet(newDone, streamMode)
00785:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 462, in _updateOutputCoordSet
00786:       self.readCoordsFromMics(outputDir, micDoneList, outputCoords)
00787:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/protocols/protocol_cryolo_picking.py", line 236, in readCoordsFromMics
00788:       convert.readMicrographCoords(mic, outputCoords, coordsFile, boxSize,
00789:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/convert.py", line 182, in readMicrographCoords
00790:       for x, y, score in reader.iterCoords():
00791:   RuntimeError: generator raised StopIteration
00792:   ------------------- PROTOCOL FAILED (DONE 9/1615)



Any suggestion?

Thank you


Sincerely,
Dmitry