Scipion does not save class from 3dClassification

[gilcantero]

When I clicked on the eye of "analyze results" to see the table with number of particles, slices, etc in the results of a 3D classification, the window was blocked for 15 minutes or so. I killed manually scipion from the console and when I try to visualize it, it opens but shows 0 as the number of particles for all the classes and I cannot save the particles of a certain class. I guess it has something to do with the database maybe? Is there any way to solve it?

Thanks, David.

[pconesa]

Thanks @gilcantero Is this scipion2 (Diocletian) or 3?

[gilcantero]

scipion 2

[pconesa]

Is this a relion 3d classification?

[gilcantero]

yes, from relion

[gilcantero]

This is the output of the terminal when pressing the eye and the table appears:

java -Xmx20g -d64 -Djava.library.path=/home/virus/SOFTWARE/SCIPION/scipion2/software/em/xmipp/lib -Dplugins.dir=/home/virus/SOFTWARE/SCIPION/scipion2/software/em/xmipp/bindings/java/imagej/plugins -cp /usr/lib64/jvm/java-1.8.0-openjdk-1.8.0/lib/:/home/virus/SOFTWARE/SCIPION/scipion2/software/em/xmipp/bindings/java/imagej/:/home/virus/SOFTWARE/SCIPION/scipion2/software/em/xmipp/bindings/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/030165_ProtRelionClassify3D/extra/relion_it022_classes_scipion.sqlite" --render _representative._filename --labels id _size --zoom 100 --visible enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size desc --order enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --mode metadata --scipion 40643 30165 30146

[pconesa]

This is showing iteration 22,can you try to show iteration 21?

[gilcantero]

It arise thise error in a window: Error: XMIPP_ERROR 36: Error in SQL of MetaData operations Error accessing table code: 5 message:database is locked. SQL command SELECT name FROM sqlite_master WHERE type='table' LIMIT 1; File: core/metadata_sql.cpp line: 1244

y esto en terminal: java -Xmx20g -d64 -Djava.library.path=/home/virus/SOFTWARE/SCIPION/scipion2/soft ware/em/xmipp/lib -Dplugins.dir=/home/virus/SOFTWARE/SCIPION/scipion2/software/e m/xmipp/bindings/java/imagej/plugins -cp /usr/lib64/jvm/java-1.8.0-openjdk-1.8.0 /lib/:/home/virus/SOFTWARE/SCIPION/scipion2/software/em/xmipp/bindings/java/ima gej/:/home/virus/SOFTWARE/SCIPION/scipion2/software/em/xmipp/bindings/java/lib/ * xmipp.viewer.scipion.ScipionViewer -i "Runs/030165_ProtRelionClassify3D/extra/ relion_it021_classes_scipion.sqlite" --render _representative._filename --labels id _size --zoom 100 --visible enabled id _size _representative._filename _rlncl assDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size de sc --order enabled id _size _representative._filename _rlnclassDistribution _rln AccuracyRotations _rlnAccuracyTranslations --mode metadata --scipion 48271 30165 30146 java.sql.SQLException: [SQLITE_BUSY] The database file is locked (database is l ocked) at org.sqlite.DB.newSQLException(DB.java:886) at org.sqlite.DB.newSQLException(DB.java:897) at org.sqlite.DB.throwex(DB.java:864) at org.sqlite.NativeDB.prepare(Native Method) at org.sqlite.DB.prepare(DB.java:207) at org.sqlite.Stmt.executeQuery(Stmt.java:186) at xmipp.viewer.scipion.ScipionMetaData.isScipionMetaData(ScipionMetaDat a.java:1242) at xmipp.viewer.scipion.ScipionViewer.openFile(ScipionViewer.java:69) at xmipp.viewer.scipion.ScipionViewer.main(ScipionViewer.java:52)

[pconesa]

There is a db lock!

Do you have enough space o the HD? (just in case)

[pconesa]

I think this can be closed. I do not think we will address this happening in Scipion2

[gilcantero]

Sin problema