Common InterMine Errors
Listed here are some common errors encountered in InterMine and some suggested fixes. See TroubleshootingTips for more information on how to find error messages.
UnsupportedClassVersionError
java.lang.UnsupportedClassVersionError: org/intermine/task/FileName (Unsupported major.minor version 49.0)
This means that your version of Java is too old, you need at least Java 1.5 to run InterMine.
can't open datasource
java.lang.RuntimeException: can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.flatmodeunittest, ...
Errors of this type mean there was a problem accessing a database, in this example with db.flatmodeunittest. Either the database specified in the xxx.properties file doesn't exist or the server/user/password details in the properties are incorrect.
FATAL: sorry, too many clients already
org.postgresql.util.PSQLException: Backend start-up failed: FATAL: sorry, too many clients already - for database: db.bio-fulldata-test
This occurs when the number of connections to a database exceeds the maximum configured in the postgres configuration. You need to increase the value of max_connections in the postgresql.conf file and restart postgres. Try 50 connections:
max_connections = 50
If you still experience this problem, see building a Mine.
OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
This means that a Java process hasn't been allocated enough memory to function correctly. You can increase the amount of memory by changing the -Xmx property in your ANT_OPTS environment variable. We recommend 1000M as a minimum, more is often needed during dataloading. Your ANT_OPTS variable should include the following:
> echo $ANT_OPTS -Xmx1000M -XX:MaxPermSize=256M
If you still experience this problem, see building a Mine.
OutOfMemoryError: PermGen space
java.lang.OutOfMemoryError: PermGen space
This occurs when Java has run out for PermGen space - where it stores ClassLoaders and Class definitions, etc. It can be fixed by increasing the -XX:MaxPermSize value in your ANT_OPTS environment variable, the default is 128M, trying 256M would be best. The ANT_OPTS variable should include the following:
> echo $ANT_OPTS -Xmx1000M -XX:MaxPermSize=256M
If you still experience this problem, see building a Mine.
Can't find class name [ClassName]
Exception caught: java.lang.IllegalArgumentException: Unknown class name Protein in package org.intermine.model.bio
In this example a class named Protein could not be found in the data model, this will usually arise when running a parser and attempting to create an Item for a class that does not exist. Check your sourcename_additions.xml files to see if the class is listed, only the additions files for sources lists on project.xml when ant build-db was run will be included in the data model.
Can't find keys
Caused by: java.lang.IllegalArgumentException: Unable to find keys for source protfeatures_source in file protfeatures_source_keys.properties
It is expecting to find some keys to integrate data from that source. Do you have a keys file in the bio/sources/protfeatures/resources?
Can't find antlib-int.xml
Unable to find jar:file:/home/malariamine/svn/trunk/intermine/integrate/main/dist/intermine-integrate.jar!/org/intermine/task/antlib-int.xml
This happens occasionally, probably due to a concurrency issue in the build system. Run the ANT command again and it should work.
See: TroubleshootingTips
