Howdy all,
I'm still having issues with the Illumina Plug in,
When running the job the summary window gives: Bead Summary importer Executing:
New raw bioassay -parsed 93094 lines in 2 files Preparing database for
import... Then eventually crashes with OutOfMemoryErrror: Java heap space.
I've tried upping Xmx up to 2gb under CATALINA_OPTS. and setting the Illumina
Bead Summary importer plugin max memory to 1gb, but still no luck.
Thanks in advance for your help,
Thomas
The stack trace from catalina.out is:
12:40:20,315 ERROR jobqueue:366 - Exception while starting jobs
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:2734)
at java.util.ArrayList.toArray(ArrayList.java:275)
at java.util.ArrayList.addAll(ArrayList.java:472)
at org.jaxen.expr.DefaultStep.evaluate(DefaultStep.java:164)
at org.jaxen.expr.DefaultLocationPath.evaluate(DefaultLocationPath.java:140)
at
org.jaxen.expr.DefaultAbsoluteLocationPath.evaluate(DefaultAbsoluteLocationPath.java:113)
at org.jaxen.expr.DefaultXPathExpr.asList(DefaultXPathExpr.java:102)
at org.jaxen.BaseXPath.selectNodesForContext(BaseXPath.java:674)
at org.jaxen.BaseXPath.selectNodes(BaseXPath.java:213)
at org.jaxen.BaseXPath.selectSingleNode(BaseXPath.java:234)
at org.jdom.xpath.JaxenXPath.selectSingleNode(JaxenXPath.java:153)
at
net.sf.basedb.core.PredefinedQuery.getQueryString(PredefinedQuery.java:150)
at
net.sf.basedb.core.HibernateUtil.getPredefinedQuery(HibernateUtil.java:1660)
at
net.sf.basedb.core.HibernateUtil.getPredefinedQuery(HibernateUtil.java:1646)
at net.sf.basedb.core.InternalJobQueue.run(InternalJobQueue.java:309)
at net.sf.basedb.util.timer.ThreadTimerTask$1.run(ThreadTimerTask.java:85)
at java.lang.Thread.run(Thread.java:662)
Exception in thread "Timer-1" Feb 11, 2011 12:40:56 PM unknown unknown
SEVERE: Exception invoking periodic operation:
java.lang.OutOfMemoryError: Java heap space
at java.lang.StringCoding$StringEncoder.encode(StringCoding.java:232)
at java.lang.StringCoding.encode(StringCoding.java:272)
at java.lang.String.getBytes(String.java:946)
at java.io.UnixFileSystem.getBooleanAttributes0(Native Method)
at java.io.UnixFileSystem.getBooleanAttributes(UnixFileSystem.java:228)
at java.io.File.exists(File.java:733)
at
org.apache.catalina.startup.HostConfig.checkResources(HostConfig.java:1113)
at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1342)
at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:303)
at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at
org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1337)
at
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1601)
at
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1610)
at
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1590)
at java.lang.Thread.run(Thread.java:662)
12:41:22,716 WARN DbControl:1147 - Found unclosed DbControl during finalize;
isLoggedIn = true; clientId = 5; userId = 1
java.lang.Throwable: Please check the code to make sure that DbControl.close()
is always called. Stacktrace of code that created this DbControl:
at net.sf.basedb.core.DbControl.<init>(DbControl.java:156)
at net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:320)
at org.apache.jsp.views.jobs.ajax_jsp._jspService(ajax_jsp.java:75)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:377)
at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:662)
12:41:22,717 WARN DbControl:313 - Exception during rollback in Hibernate
net.sf.basedb.core.BaseException: Transaction not successfully started
at net.sf.basedb.core.HibernateUtil.rollback(HibernateUtil.java:1070)
at net.sf.basedb.core.DbControl.rollback(DbControl.java:307)
at net.sf.basedb.core.DbControl.close(DbControl.java:265)
at net.sf.basedb.core.DbControl.finalize(DbControl.java:1155)
at java.lang.ref.Finalizer.invokeFinalizeMethod(Native Method)
at java.lang.ref.Finalizer.runFinalizer(Finalizer.java:83)
at java.lang.ref.Finalizer.access$100(Finalizer.java:14)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:160)
Caused by: org.hibernate.TransactionException: Transaction not successfully
started
at
org.hibernate.transaction.JDBCTransaction.rollback(JDBCTransaction.java:183)
at net.sf.basedb.core.HibernateUtil.rollback(HibernateUtil.java:1066)
... 7 more
12:41:22,936 ERROR jobqueue:524 - Exception while executing job: Job[id=20;
name=Run plugin: Illumina Bead Summary importer]
net.sf.basedb.core.BaseException: Java heap space
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:518)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.OutOfMemoryError: Java heap space
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