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scipion-em / scipion-em-sphire

Plugin to use Sphire programs within the Scipion framework
GNU General Public License v3.0
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Error out of index streaming #18

Closed rsanchezgarc closed 1 year ago

rsanchezgarc commented 5 years ago

I am getting this error when continuing the protocol. I guess that it happens when the batch size for streaming is not divisible

01800: File "/usr/local/scipion/2.0-devel/scipion/pyworkflow/protocol/protocol.py", line 186, in run 01801: self._run() 01802: File "/usr/local/scipion/2.0-devel/scipion/pyworkflow/protocol/protocol.py", line 237, in _run 01803: resultFiles = self._runFunc() 01804: File "/usr/local/scipion/2.0-devel/scipion/pyworkflow/protocol/protocol.py", line 233, in _runFunc 01805: return self._func(self._args) 01806: File "/usr/local/scipion/2.0-devel/scipion/pyworkflow/em/protocol/protocol_particles_picking.py", line 280, in pickMicrographListStep 01807: self._pickMicrographList(micList, args) 01808: File "/usr/local/scipion/2.0-devel/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_picking.py", line 169, in _pickMicrographList 01809: workingDir = self._getTmpPath(self.getMicsWorkingDir(micList)) 01810: File "/usr/local/scipion/2.0-devel/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolopicking.py", line 257, in getMicsWorkingDir 01811: wd = 'micrographs%s' % micList[0].strId() 01812: IndexError: list index out of range 01813: Protocol failed: list index out of range 01814: FAILED: pickMicrographListStep, step 19

delarosatrevin commented 3 years ago

I'm still experiencing this issue, any progress???

pyworkflow: 3.0.7
plugin: sphire
plugin v: 3.0.5
pconesa commented 3 years ago

Thanks both! We need to look at this

JorMaister commented 3 years ago

Thanks both for reporting. @delarosatrevin, does the problem persist in plugin version 3.0.6? @rsanchezgarc, which version of the plugin are you using?

delarosatrevin commented 3 years ago

@JorMaister I don't have time now to test with the new plugin version, but I have seen a similar error message in Relion streaming protocols. So it might be in the base code.