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Re: [scipion-users] Xmipp viewer issue
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From: Erik Ž. <eri...@gm...> - 2018-07-13 09:10:20
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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 > > |
