[scipion-users] Cryosparc CryoSPARC 2+ .cs file error

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

Dear colleagues,

The cryosparc global CTF fails in SCIPION 3 (but finished correctly in cryosparc itself) with the following error — CryoSPARC 2+ .cs file

FINISHED: processStep, step 2, time 2021-03-08 14:12:20.142810
00037:   STARTED: createOutputStep, step 3, time 2021-03-08 14:12:20.173650
00038:   Detected CryoSPARC 2+ .cs file
00039:   Traceback (most recent call last):
00040:     File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run
00041:       self._run()
00042:     File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run
00043:       resultFiles = self._runFunc()
00044:     File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc
00045:       return self._func(*self._args)
00046:     File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 227, in createOutputStep
00047:       convertCs2Star(args)
00048:     File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/cryosparc2/convert/convert.py", line 51, in convertCs2Star
00049:       cs = np.load(args.input[0])
00050:     File "/opt/Scipion3/.scipion3env/lib64/python3.6/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/005994_ProtCryoSparcGlobalCtfRefinement/extra/J102/particles.cs'
00053:   Protocol failed: [Errno 2] No such file or directory: 'Runs/005994_ProtCryoSparcGlobalCtfRefinement/extra/J102/particles.cs'
00054:   FAILED: createOutputStep, step 3, time 2021-03-08 14:12:22.171112
00055:   *** Last status is failed 
00056:   ------------------- PROTOCOL FAILED (DONE 3/3)


Any advice?


Thank you in advance!

Sincerely,
Dmitry