[scipion-users] SCIPION3 error -- Cryosparc -- crysparc2 – global ctf

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

Dear Yunior, dear colleagues,

 

I hope you could help me.

 

Error in SCIPION3 during crysparc2 – global ctf refinement.

 

When I change the “Number of iterations” parameter in the crysparc2 – global ctf refinement to 2…or.4…or….8….(more than 1) SCIPION3 gives the error:

 

 

00037:   STARTED: createOutputStep, step 3, time 2021-03-17 14:22:18.663183

00038:   Detected CryoSPARC 2+ .cs file

00039:   Traceback (most recent call last):

00040:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 189, in run

00041:       self._run()

00042:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run

00043:       resultFiles = self._runFunc()

00044:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc

00045:       return self._func(*self._args)

00046:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 227, in createOutputStep

00047:       convertCs2Star(args)

00048:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 51, in convertCs2Star

00049:       cs = np.load(args.input[0])

00050:     File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 428, in load

00051:       fid = open(os_fspath(file), "rb")

00052:   FileNotFoundError: [Errno 2] No such file or directory: 'Runs/006620_ProtCryoSparcGlobalCtfRefinement/extra/J87/particles.cs'

00053:   Protocol failed: [Errno 2] No such file or directory: 'Runs/006620_ProtCryoSparcGlobalCtfRefinement/extra/J87/particles.cs'

00054:   FAILED: createOutputStep, step 3, time 2021-03-17 14:22:21.455791

00055:   *** Last status is failed

 

 

BUT inside the cryosparc the process finishes without error.

Please see the image.

 

 

When I use 1 (default) value in crysparc2 – global ctf refinement SCIPION3 finishes with no error.

 

What can be the solution for that?

 

 

 

Sincerely,

Dmitry