Hello,
I have added some data to our customised Ensembl mart and I am trying
to rebuild it now. However, when I update all schemas in MartBuilder,
then accept all changes and finally try to generate the SQL for the
mart, the exceptions as shown below occur. Please note that even
though the top of the call stacks says 'MartScript' rather than
'MartBuilder', it is the same underlying code of MartBuilder that gets
executed. I just wrote a scripting front-end that takes me through the
mart creation process, which I would otherwise have to do by hand.
At first I thought there was a network connection problem regarding
the MySQL database, but since this exception reoccurred, I begin to
doubt that. Could this be related to the extended amount of time
MartBuilder needs to pick up the tables that I have added to Ensembl?
It takes about 7h for MartBuilder to calculate the database changes
once I have clicked 'Update all schemas'.
com.mysql.jdbc.CommunicationsException: Communications link failure
due to underlying exception:
** BEGIN NESTED EXCEPTION **
java.io.EOFException
STACKTRACE:
java.io.EOFException
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
at com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428)
at com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at
com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882)
at
org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java:1773)
at
org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema.java:1787)
at
org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1818)
at
org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319)
at
org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter.java:1662)
at
org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterpreter.java:273)
at
org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34)
at
org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116)
at org.bergmanlab.martscript.MartScript.main(MartScript.java:72)
** END NESTED EXCEPTION **
Last packet sent to the server was 204460 ms ago.
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2592)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
at com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428)
at com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at
com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882)
at
org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java:1773)
at
org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema.java:1787)
at
org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1818)
at
org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319)
at
org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter.java:1662)
at
org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterpreter.java:273)
at
org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34)
at
org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116)
at org.bergmanlab.martscript.MartScript.main(MartScript.java:72)
Woops.. the following exception occurred during the script's exception:
java.sql.SQLException: No operations allowed after connection
closed.Connection was implicitly closed due to underlying
exception/error:
** BEGIN NESTED EXCEPTION **
com.mysql.jdbc.CommunicationsException
MESSAGE: Communications link failure due to underlying exception:
** BEGIN NESTED EXCEPTION **
java.io.EOFException
STACKTRACE:
java.io.EOFException
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
at com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428)
at com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at
com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882)
at
org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java:1773)
at
org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema.java:1787)
at
org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1818)
at
org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319)
at
org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter.java:1662)
at
org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterpreter.java:273)
at
org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34)
at
org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116)
at org.bergmanlab.martscript.MartScript.main(MartScript.java:72)
** END NESTED EXCEPTION **
Last packet sent to the server was 204460 ms ago.
STACKTRACE:
com.mysql.jdbc.CommunicationsException: Communications link failure
due to underlying exception:
** BEGIN NESTED EXCEPTION **
java.io.EOFException
STACKTRACE:
java.io.EOFException
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
at com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428)
at com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at
com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882)
at
org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java:1773)
at
org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema.java:1787)
at
org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1818)
at
org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319)
at
org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter.java:1662)
at
org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterpreter.java:273)
at
org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34)
at
org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116)
at org.bergmanlab.martscript.MartScript.main(MartScript.java:72)
** END NESTED EXCEPTION **
Last packet sent to the server was 204460 ms ago.
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2592)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
at com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428)
at com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916)
at
com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79)
at
com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882)
at
org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java:1773)
at
org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema.java:1787)
at
org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1818)
at
org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319)
at
org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter.java:1662)
at
org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterpreter.java:273)
at
org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34)
at
org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116)
at org.bergmanlab.martscript.MartScript.main(MartScript.java:72)
** END NESTED EXCEPTION **
at com.mysql.jdbc.Connection.checkClosed(Connection.java:1844)
at com.mysql.jdbc.Connection.createStatement(Connection.java:2872)
at com.mysql.jdbc.Connection.createStatement(Connection.java:2854)
at
com.mysql.jdbc.Connection.getMetadataSafeStatement(Connection.java:3440)
at com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4422)
at
org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1409)
at
org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter.java:1662)
at
org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterpreter.java:273)
at
org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34)
at
org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116)
at org.bergmanlab.martscript.MartScript.main(MartScript.java:72)
BW,
Joachim
--
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Faculty of Life Sciences
The University of Manchester
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