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Re: [scipion-users] Xmipp viewer issue
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From: Gregory S. <sha...@gm...> - 2018-07-13 13:33:13
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Hi Erik, You are editing the wrong file, you should check the ~/. config/scipion/scipion.conf. It should contain RELION_HOME=%(EM_ROOT)s/relion-1.4 Did you install relion through scipion or separately? If it was installed separately, relion-1.4 link should point to relion installation folder. Also, have you tried to run relion outside of Scipion? On Fri, Jul 13, 2018, 10:10 Erik Župa <eri...@gm...> wrote: > Thanks for advice but I have already tried this thing and it is not > working. I tried to use RELION_HOME=%(EM_ROOT)s/relion-1.4, I also tried > the write whole pathway RELION_HOME = > /home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/relion-1.4 > but the result is same. If I try to run configuration of Scipion with both > cases I get this "In section BUILD, option RELION_HOME exists in the > configuration file but not in the template." > > > Erik Zupa > > On Thu, Jul 12, 2018 at 2:07 PM, Gregory Sharov <sha...@gm...> > wrote: > >> In ~/.config/scipion/scipion.conf there is a line pointing to scipion >> EM_ROOT folder (you should adjust version name to the one you have), i.e.: >> RELION_HOME=%(EM_ROOT)s/relion-1.4 >> >> It points to scipion/software/em/relion-1.4 which could be a symbolic >> link to whatever path you have installed relion. >> >> Please have a look at >> https://github.com/I2PC/scipion/wiki/Installing-EM-Packages#linking-to-existing-package-installations >> >> 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 267542 >> e-mail: gs...@mr... >> >> >> On Thu, Jul 12, 2018 at 1:01 PM Erik Župa <eri...@gm...> wrote: >> >>> 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 >>>> >>>> >>> >>> ------------------------------------------------------------------------------ >>> 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 > |
