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I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.i2pc.es
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'scipion - join sets' fails when joining large sets of coordinates #2061

Closed JuhaHuiskonen closed 4 years ago

JuhaHuiskonen commented 4 years ago

I am trying to join two sets of coordinates (from CrYOLO runs that complete ok) with 1M and 2.8M coordinates. This fails with the following error:

00001: RUNNING PROTOCOL ----------------- 00002: HostName: puhti-login1.bullx 00003: PID: 151118 00004: Scipion: v2.0 (2019-04-23) Diocletian 00005: currentDir: /scratch/project_2001566/ScipionUserData/projects/JK_em20223-30 00006: workingDir: Runs/005526_ProtUnionSet 00007: runMode: Continue 00008: MPI: 1 00009: threads: 1 00010: len(steps) 1 len(prevSteps) 0 00011: Starting at step: 1 00012: Running steps 00013: STARTED: createOutputStep, step 1 00014: 2019-10-27 16:12:34.015138 00015: Traceback (most recent call last): 00016: File "/projappl/project_2001566/apps/scipion/2.0/pyworkflow/protocol/protocol.py", line 186, in run 00017: self._run() 00018: File "/projappl/project_2001566/apps/scipion/2.0/pyworkflow/protocol/protocol.py", line 237, in _run 00019: resultFiles = self._runFunc() 00020: File "/projappl/project_2001566/apps/scipion/2.0/pyworkflow/protocol/protocol.py", line 233, in _runFunc 00021: return self._func(*self._args) 00022: File "/projappl/project_2001566/apps/scipion/2.0/pyworkflow/em/protocol/protocol_sets.py", line 138, in createOutputStep 00023: outputSet = getattr(self, "_create%s" % set1.getClassName())() 00024: TypeError: _createSetOfCoordinates() takes at least 2 arguments (1 given) 00025: Protocol failed: _createSetOfCoordinates() takes at least 2 arguments (1 given) 00026: FAILED: createOutputStep, step 1 00027: 2019-10-27 16:12:34.057002 00028: *** Last status is failed 00029: ------------------- PROTOCOL FAILED (DONE 1/1)

Our Scipion version is 2.0

pconesa commented 4 years ago

Hi @JuhaHuiskonen , thanks for reporting the issue. We have already fixed it in our devel branch, but it might not be a good idea to switch to it for production work.

the changes are here: https://github.com/I2PC/scipion/commit/e9381a5823d19398e75d9a5d80ce53c5dd8e3ec0#diff-6f8bea850795c9016fc4a7754c247bfc

1.- Either make the same change to your local file 2.- Do the extraction first and then join particles.

JuhaHuiskonen commented 4 years ago

@pconesa, thanks this worked!

pconesa commented 4 years ago

I'm closing this issue. Feel free to reopen it if I'm wrong or missed something.