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Re: [scipion-users] 2Dclasses with millions of particles
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From: Carlos O. S. S. <co...@cn...> - 2019-07-12 22:27:00
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Dear Ipsita, you may also want to try deep consensus. If you have several pickings, it is quite easy. If not, you can pick noise particles (Ctrl-F, noise), extract them and teach the deep consensus (Ctrl-F, deep) what is a particle and what is not. Make sure that you have the deepToolKit installed. Kind regards, Carlos Oscar El 12/07/2019 a las 12:52, Ipsita Banerjee escribió: > Hi > > This is just a query. I have been trying to screen my particles using > Xmipp3 particle screening since the last 2 to 3 days… I am using the > installation of Scipion on Kebnekaise cluster. However, this process > is taking a very, very long time… > I am submitting the job in the queue and even gave 24 hours, but the > job did not finish.. > > I just wanted to ask whether there is any way to speed up this process > or am I doing something wrong? > > Thanks so much for all the help.. > > Best regards, > Ipsita > >> On 9 Jul 2019, at 05:54, Carlos Oscar S. Sorzano <co...@CN... >> <mailto:co...@CN...>> wrote: >> >> Dear Ipsita, >> >> another way of cleaning the set of particles is using deep consensus >> if you have several pickings on the same data. This protocol works at >> the level of coordinates so it should not be so much affected by >> memory issues. For using this protocol, make sure you have installed >> in the plugins the deepLearningToolkit under the Xmipp plugin. >> >> Kind regards, Carlos Oscar >> >> El 08/07/2019 a las 16:07, Ipsita Banerjee escribió: >>> Hi >>> >>> Today, after increasing the memory space, I tried to open the >>> classification in scipion, but after 10 mins I get this error.. >>> >>> md.sort(sortByLabel) >>> XmippError: Error code: 21 message: no such table: MDTable_2 >>> Sqlite query: INSERT INTO MDTable_3( "rlnEnabled", >>> "rlnCoordinateX", "rlnCoordinateY", "rlnMicrographName", >>> "rlnMicrographId", "rlnImageId", "rlnImageName", "rlnPhaseShift", >>> "rlnDefocusU", "rlnDefocusV", "rlnDefocusAngle", >>> "rlnAmplitudeContrast", "rlnSphericalAberration", "rlnVoltage", >>> "rlnGroupName", "rlnGroupNumber", "rlnAngleRot", "rlnAngleTilt", >>> "rlnAnglePsi", "rlnOriginX", "rlnOriginY", "rlnClassNumber", >>> "rlnNormCorrection", "rlnLogLikeliContribution", >>> "rlnMaxValueProbDistribution", "rlnNrOfSignificantSamples") SELECT >>> "rlnEnabled", "rlnCoordinateX", "rlnCoordinateY", >>> "rlnMicrographName", "rlnMicrographId", "rlnImageId", >>> "rlnImageName", "rlnPhaseShift", "rlnDefocusU", "rlnDefocusV", >>> "rlnDefocusAngle", "rlnAmplitudeContrast", "rlnSphericalAberration", >>> "rlnVoltage", "rlnGroupName", "rlnGroupNumber", "rlnAngleRot", >>> "rlnAngleTilt", "rlnAnglePsi", "rlnOriginX", "rlnOriginY", >>> "rlnClassNumber", "rlnNormCorrection", "rlnLogLikeliContribution", >>> "rlnMaxValueProbDistribution", "rlnNrOfSignificantSamples" FROM >>> MDTable_2 >>> >>> So, now I am trying to clean my particles with Xmipp screening >>> particles. >>> >>> Thanks and best regards, >>> Ipsita >>> >>>> On 8 Jul 2019, at 08:54, Pablo Conesa <pc...@CN... >>>> <mailto:pc...@CN...>> wrote: >>>> >>>> Hi, try to increase java memory setting >>>> JAVA_MAX_MEMORY = 3 >>>> >>>> In your <scipion home>/config/scipion.conf >>>> >>>> Additionally, try to prune/clean you set as soon as possible. >>>> >>>> Xmipp screening particles could be usefull to reject bad ones at >>>> the begining. >>>> >>>> >>>> El 5 jul. 2019 21:32, Ipsita Banerjee >>>> <ips...@bi... >>>> <mailto:ips...@bi...>> escribió: >>>> >>>> Dear Scipion Users, >>>> >>>> I have a dataset where I have about 2 million picked >>>> particles.. I could run relion2D classification for these >>>> particles.. >>>> However, when I click on the Analyze results button, and try to >>>> open the tab "Show classification in Scipion", I don't see >>>> anything.. >>>> When i click on the tab "show classes only", I can see the >>>> classes only.. >>>> Please, I need some help as to what I can do to continue with >>>> the processing... >>>> >>>> Thanks so much... >>>> >>>> Best regards, >>>> Ipsita >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> <mailto:sci...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> -- >> ------------------------------------------------------------------------ >> Carlos Oscar Sánchez Sorzano e-mail:co...@cn... >> Biocomputing unithttp://i2pc.es/coss >> National Center of Biotechnology (CSIC) >> c/Darwin, 3 >> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >> ------------------------------------------------------------------------ >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://i2pc.es/coss National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
