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Re: [scipion-users] 2Dclasses with millions of particles
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From: Ipsita B. <ips...@bi...> - 2019-07-12 10:52:47
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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...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn...<mailto: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 ------------------------------------------------------------------------ _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
