bridgedb
have GdbConstructImpl3.createGdbIndices() report what it's doing when Exceptions happen internally
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.
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...
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.
Tried the whole thing again - whole process from downloading vcf variation files from ensembl until variantCreator. Same error... Help!