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Re: [scipion-users] SCIPON 2--> SCIPION 3.0 relion-motioncor
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From: Dmitry S. <Sem...@gm...> - 2020-11-30 16:15:33
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Dear Grigory, I guess I spotted the issue — the original files were stored under the symbolic link (in the protocol — import movies) and later were removed from there. So that possibly cased the issue. Please let me fix it — I will report if that was the case. Thank you! Sincerely, Dmitry > On 30. Nov 2020, at 16:20, Grigory Sharov <sha...@gm...> wrote: > > Hi Dmitry, > > could you please send me: > > - Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star , > - first hundred lines of Runs/037414_ProtRelionBayesianPolishing/input_particles.star and > - any star file from Runs/037414_ProtRelionBayesianPolishing/input/ folder? > > then we can go from there. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Mon, Nov 30, 2020 at 3:13 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > 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 > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
