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bridgedb / BridgeDb

The BridgeDb Library source code
https://bridgedb.org/
Apache License 2.0
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have GdbConstructImpl3.createGdbIndices() report what it's doing when Exceptions happen internally #167

Closed fehrhart closed 1 year ago

fehrhart commented 5 years ago

The error message occured when using the VariantCreatorv.1.1 on the datasets Missense and PTV_Missense at the very end of process. The other datasets went through without problems (Exonic, Polyphen, PTV).

Link to tutorial: https://docs.google.com/document/d/1TxzubfLtXquBb7AZDul4E3-7e-O0I62ZnXtztguabZM/edit

Link to files involved (java scripts, config file, data files): https://drive.google.com/drive/folders/1BEdc9DBcuDQnwieDkcDR7wfRlaPb03ys

Error message:

6510000
6511000
6512000
Thu May 16 10:54:03 CEST 2019
Start to the creation of the database, might take some time
Exception in thread "main" java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: org.bridgedb.IDMapperException: java.sql.SQLException: Java exception: 'Illegal Capacity: -19860521: java.lang.IllegalArgumentException'.
        at org.bridgedb.rdb.construct.GdbConstructImpl3.createGdbIndices(GdbConstructImpl3.java:214)
        at org.bridgedb.rdb.construct.GdbConstructImpl3.finalize(GdbConstructImpl3.java:43)
        at org.bridgedb.creator.DbBuilder.finalizeDb(DbBuilder.java:128)
        at VariantCreator.merge(VariantCreator.java:160)
        at VariantCreator.main(VariantCreator.java:54)
        ... 5 more
Caused by: java.sql.SQLException: Java exception: 'Illegal Capacity: -19860521: java.lang.IllegalArgumentException'.
        at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
        at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
        at org.apache.derby.impl.jdbc.Util.javaException(Unknown Source)
        at org.apache.derby.impl.jdbc.TransactionResourceImpl.wrapInSQLException(Unknown Source)
        at org.apache.derby.impl.jdbc.TransactionResourceImpl.handleException(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection.handleException(Unknown Source)
        at org.apache.derby.impl.jdbc.ConnectionChild.handleException(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedStatement.executeStatement(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedStatement.execute(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedStatement.execute(Unknown Source)
        at org.bridgedb.rdb.construct.GdbConstructImpl3.createGdbIndices(GdbConstructImpl3.java:199)
        ... 9 more
Caused by: java.sql.SQLException: Java exception: 'Illegal Capacity: -19860521: java.lang.IllegalArgumentException'.
        at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
        at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
        ... 20 more
Caused by: java.lang.IllegalArgumentException: Illegal Capacity: -19860521
        at java.util.Vector.<init>(Unknown Source)
        at java.util.Vector.<init>(Unknown Source)
        at org.apache.derby.impl.store.access.sort.MergeSort.multiStageMerge(Unknown Source)
        at org.apache.derby.impl.store.access.sort.MergeSort.openSortRowSource(Unknown Source)
        at org.apache.derby.impl.store.access.RAMTransaction.openSortRowSource(Unknown Source)
        at org.apache.derby.impl.sql.execute.CreateIndexConstantAction.loadSorter(Unknown Source)
        at org.apache.derby.impl.sql.execute.CreateIndexConstantAction.executeConstantAction(Unknown Source)
        at org.apache.derby.impl.sql.execute.MiscResultSet.open(Unknown Source)
        at org.apache.derby.impl.sql.GenericPreparedStatement.execute(Unknown Source)
        ... 13 more
egonw commented 5 years ago

Okay, well, at least I can say this is not a BridgeDb problem. It's the negative vector length that causes the problem. Furthermore, it seems to me it's deep inside Derby. We can check next week if this happens specifically with the most recent Derby version or the previous one we used. But I think you're just hit the limits of what Derby can handle...

fehrhart commented 5 years ago

Interesting... It should not be the size of the total file, Exonic collection is bigger and that went through. If it is variant length, there should be a script that cuts them. I observed no cut-off reports in the Missense file - but in the PTV_Missense. Maybe there is a missense variant that blocks it.

fehrhart commented 5 years ago

Tried the whole thing again - whole process from downloading vcf variation files from ensembl until variantCreator. Same error... Help!

fehrhart commented 4 years ago

Is this issue still relevant? @egonw

egonw commented 1 year ago

We do not provide these mapping files anymore.