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Re: [scipion-users] Xmipp viewer issue
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From: Erik Ž. <eri...@gm...> - 2018-07-12 12:01:40
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My config file is totally missing RELION_HOME despite the relion package was installed. How do I set RELION_HOME? Erik Zupa On Thu, Jul 12, 2018 at 1:28 PM, Gregory Sharov <sha...@gm...> wrote: > Hi Erik, > > It looks like 'which relion_refine_mpi' returns nothing. Do you have a > correct RELION_HOME set in config file? Did you try running relion with mpi > outside of scipion? > > On Thu, Jul 12, 2018, 12:04 Erik Župa <eri...@gm...> wrote: > >> I solved the problem of particle extraction window. It was wrong Java >> path. However, my relion 2D classification is not working, Scipion is >> showing this Error >> >> Erik Zupa >> >> 00021: mpirun: Error: unknown option "--tau2_fudge" >> 00022: Type 'mpirun --help' for usage. >> 00023: Traceback (most recent call last): >> 00024: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/pyworkflow/protocol/protocol.py", line 182, in run >> 00025: self._run() >> 00026: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/pyworkflow/protocol/protocol.py", line 228, in _run >> 00027: resultFiles = self._runFunc() >> 00028: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/pyworkflow/protocol/protocol.py", line 224, in _runFunc >> 00029: return self._func(*self._args) >> 00030: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py", line >> 789, in runRelionStep >> 00031: self.runJob(self._getProgram(), params) >> 00032: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/pyworkflow/protocol/protocol.py", line 1077, in runJob >> 00033: self._stepsExecutor.runJob(self._log, program, arguments, >> **kwargs) >> 00034: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/pyworkflow/protocol/executor.py", line 56, in runJob >> 00035: env=env, cwd=cwd) >> 00036: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/pyworkflow/utils/process.py", line 51, in runJob >> 00037: return runCommand(command, env, cwd) >> 00038: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/pyworkflow/utils/process.py", line 65, in runCommand >> 00039: check_call(command, shell=True, stdout=sys.stdout, >> stderr=sys.stderr, env=env, cwd=cwd) >> 00040: File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_ >> linux64/scipion/software/lib/python2.7/subprocess.py", line 540, in >> check_call >> 00041: raise CalledProcessError(retcode, cmd) >> 00042: CalledProcessError: Command 'mpirun -np 3 -bynode `which >> relion_refine_mpi` --tau2_fudge 2 --scale --iter 25 --norm >> --memory_per_thread 2 --ctf --offset_range 5.0 --oversampling 1 --o >> Runs/003210_ProtRelionClassify2D/extra/relion --i Runs/003210_ >> ProtRelionClassify2D/input_particles.star --particle_diameter 210.0 --K >> 3 --psi_step 10.0 --ctf_phase_flipped --flatten_solvent --zero_mask >> --offset_step 2.0 --angpix 3.0 --j 1' returned non-zero exit status 213 >> 00043: Protocol failed: Command 'mpirun -np 3 -bynode `which >> relion_refine_mpi` --tau2_fudge 2 --scale --iter 25 --norm >> --memory_per_thread 2 --ctf --offset_range 5.0 --oversampling 1 --o >> Runs/003210_ProtRelionClassify2D/extra/relion --i Runs/003210_ >> ProtRelionClassify2D/input_particles.star --particle_diameter 210.0 --K >> 3 --psi_step 10.0 --ctf_phase_flipped --flatten_solvent --zero_mask >> --offset_step 2.0 --angpix 3.0 --j 1' returned non-zero exit status 213 >> >> On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...> >> wrote: >> >>> is java in your path? >>> >>> what happens if you type in the "console/terminal": >>> >>> java -version >>> >>> >>> >>> On 09/07/18 14:39, David Maluenda wrote: >>> >>> Ouch.. strange.. >>> >>> What appears as Output for the Xmipp-ExtractParticles? Could the output >>> set be empty? >>> The summary tab (in the scipion GUI) should display: >>> >>> *Name-of-the-protocol* -> outputParticles SetOfParticles (* >>> # items*, ** x **, **.* A/px ) >>> >>> Then, the number of items # is bigger than 0? >>> >>> <http://ucm.es/> >>> >>> *_____ Dr. David Maluenda Niubó* >>> dma...@cn... - (+34) 619 029 310 >>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> >>> BioComputing Unit <http://biocomputingunit.es/> >>> >>> This email message and any documents attached to it may contain >>> confidential or legally protected material and are intended solely for the >>> use of the individual or organization to whom they are addressed. We remind >>> you that if you are not the intended recipient of this email message or the >>> person responsible for processing it, then you are not authorized to read, >>> save, modify, send, copy or disclose any of its contents. If you have >>> received this email message by mistake, we kindly ask you to inform the >>> sender of this and to eliminate both the message and any attachments it >>> carries from your account. Thank you for your collaboration. >>> >>> >>> >>> On Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote: >>> >>>> Hi David, >>>> >>>> I am not receiving any error messages from Scipion after the command. >>>> However, there is no new window popping out after the command. >>>> >>>> Erik Zupa >>>> >>>> >>>> On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...> >>>> wrote: >>>> >>>>> Hi Erik, >>>>> >>>>> This is the command that Scipion launch to open the viewer and it >>>>> looks fine.. so, it should open a window with the particles... >>>>> >>>>> Is there any error message after the command that you are reporting? >>>>> >>>>> Thanks! >>>>> >>>>> <http://ucm.es/> >>>>> >>>>> *_____ Dr. David Maluenda Niubó* >>>>> dma...@cn... - (+34) 619 029 310 >>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> >>>>> BioComputing Unit <http://biocomputingunit.es/> >>>>> >>>>> This email message and any documents attached to it may contain >>>>> confidential or legally protected material and are intended solely for the >>>>> use of the individual or organization to whom they are addressed. We remind >>>>> you that if you are not the intended recipient of this email message or the >>>>> person responsible for processing it, then you are not authorized to read, >>>>> save, modify, send, copy or disclose any of its contents. If you have >>>>> received this email message by mistake, we kindly ask you to inform the >>>>> sender of this and to eliminate both the message and any attachments it >>>>> carries from your account. Thank you for your collaboration. >>>>> >>>>> >>>>> >>>>> On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote: >>>>> >>>>>> Hello colleagues, >>>>>> >>>>>> >>>>>> I have problem to analyze results of extracting of particles. I >>>>>> successfully ran xmipp3- extract particles. However, I cannot analyze >>>>>> results because everytime I try, Scipion come with something like this: >>>>>> >>>>>> >>>>>> java -Xmx2g -d64 -Djava.library.path=/home/ >>>>>> erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib >>>>>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017- >>>>>> 06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins -cp >>>>>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26. >>>>>> x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017- >>>>>> 06-14_linux64/scipion/software/em/xmipp/external/ >>>>>> imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017- >>>>>> 06-14_linux64/scipion/software/em/xmipp/java/lib/* >>>>>> xmipp.viewer.scipion.ScipionViewer -i "Runs/002809_ >>>>>> XmippProtExtractParticles/particles.sqlite" --visible id enabled >>>>>> _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling >>>>>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle >>>>>> _transform._matrix --order id enabled _index _filename _xmipp_zScore >>>>>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV >>>>>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby >>>>>> _xmipp_zScore asc --scipion 55971 2856 >>>>>> >>>>>> >>>>>> I am thankful for any help. >>>>>> >>>>>> Erik Zupa >>>>>> >>>>>> CEITEC Brno Czech Republic >>>>>> ------------------------------------------------------------ >>>>>> ------------------ >>>>>> Check out the vibrant tech community on one of the world's most >>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ >>>>>> _________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> >>>>> >>>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ >> _________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
