[scipion-users] SCIPON 2--> SCIPION 3.0 relion-motioncor

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

Dear colleagues,

 

A compatibility question:

 

I have a project done by SCIPION 2.0: including relion particle polishing  

 Now when I open it with SCIPION 3.0 all works fine except Bayesian polishing.


The error is :

Using dose per frame from Runs/037414_ProtRelionBayesianPolishing/input/FoilHole_15002836_Data_15054168_15054170_20200615_191823_Fractions.star: 1 e/A^2

02673:   in: /home/user/Data/Software/Scipion3/software/em/relion-3.1.0/src/jaz/micrograph_handler.cpp, line 211

02674:   ERROR:

02675:   ERROR: Not a single movie contains the requested number of frames (119)

02676:   === Backtrace  ===

02677:   relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x453571]

02678:   relion_motion_refine(_ZN17MicrographHandler20findLongEnoughMoviesERKSt6vectorI13MetaDataTableSaIS1_EEii+0x44d) [0x53272d]

02679:   relion_motion_refine(_ZN13MotionRefiner4initEv+0xee3) [0x47db43]

02680:   relion_motion_refine(main+0x31) [0x428841]

02681:   /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd0b7c19555]

02682:   relion_motion_refine() [0x42955f]

02683:   ==================

02684:   ERROR:

02685:   ERROR: Not a single movie contains the requested number of frames (119)

02686:   Traceback (most recent call last):

02687:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 187, in run

02688:       self._run()

02689:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run

02690:       resultFiles = self._runFunc()

02691:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc

02692:       return self._func(*self._args)

02693:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 309, in trainOrPolishStep

02694:       self.runJob(prog, args)

02695:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1338, in runJob

02696:       self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)

02697:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob

02698:       process.runJob(log, programName, params,

02699:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 51, in runJob

02700:       return runCommand(command, env, cwd)

02701:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 66, in runCommand

02702:       check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,

02703:     File "/home/user/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", line 364, in check_call

02704:       raise CalledProcessError(retcode, cmd)

02705:   subprocess.CalledProcessError: Command 'relion_motion_refine --i Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o Runs/037414_ProtRelionBayesianPolishing/extra --f Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1.

02706:   Protocol failed: Command 'relion_motion_refine --i Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o Runs/037414_ProtRelionBayesianPolishing/extra --f Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1.

02707:   FAILED: trainOrPolishStep, step 2, time 2020-11-30 16:07:27.531346

02708:   *** Last status is failed

02709:   ------------------- PROTOCOL FAILED (DONE 2/2)

 

 

Could that be a consequence that the motion correction was done in relion-motioncor protocol in SCIPION 2.0 and SCIPION 3.0 has the newer relion-motion correction protocol? (The indirect sign I see in the output relion-motioncor file).

 

Thank you in advance.

 

Sincerely,

Dmitry