Re: [scipion-users] 2Dclasses with millions of particles

[Carlos O. S. S. <co...@cn...>]

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
>>
>>
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>
>
>
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-- 
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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
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