Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
Windows v9967 IGB 1GB
Pref -> Other options
Activate 'Confirm before loading large data set'
Local file 'DryCT2.sm.bam' (which is 1.8G)
Do not adjust zoom
Load data
Did not confirm before loading, file does not load, and error thrown in console:
Jan 25, 2012 4:05:25 PM com.affymetrix.igb.view.load.GeneralLoadUtils$2 finished
SEVERE: Unable to get refresh action result.
java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)
at java.util.concurrent.FutureTask.get(Unknown Source)
at javax.swing.SwingWorker.get(Unknown Source)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:865)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31)
at javax.swing.SwingWorker$5.run(Unknown Source)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source)
at sun.swing.AccumulativeRunnable.run(Unknown Source)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source)
at javax.swing.Timer.fireActionPerformed(Unknown Source)
at javax.swing.Timer$DoPostEvent.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: java.lang.OutOfMemoryError: Java heap space
at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:241)
at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:229)
at net.sf.samtools.SAMRecord.getBaseQualityString(SAMRecord.java:247)
at com.affymetrix.genometryImpl.symloader.XAM.convertSAMRecordToSymWithProps(XAM.java:178)
at com.affymetrix.genometryImpl.symloader.BAM.parse(BAM.java:137)
at com.affymetrix.genometryImpl.symloader.XAM.getRegion(XAM.java:122)
at com.affymetrix.igb.featureloader.QuickLoad.getRegion(QuickLoad.java:402)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:248)
at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177)
at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:906)
at com.affymetrix.igb.view.load.GeneralLoadUtils.access$200(GeneralLoadUtils.java:88)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:839)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:834)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
Windows v9967 IGB 1GB Pref -> Other options Activate 'Confirm before loading large data set Local file 'DryCT2.sm.bam' (which is 1.8G) Do not adjust zoom Load data Did not confirm before loading and error thrown in console: Jan 25, 2012 4:05:25 PM com.affymetrix.igb.view.load.GeneralLoadUtils$2 finished SEVERE: Unable to get refresh action result. java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source) at java.util.concurrent.FutureTask.get(Unknown Source) at javax.swing.SwingWorker.get(Unknown Source) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:865) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.OutOfMemoryError: Java heap space at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:241) at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:229) at net.sf.samtools.SAMRecord.getBaseQualityString(SAMRecord.java:247) at com.affymetrix.genometryImpl.symloader.XAM.convertSAMRecordToSymWithProps(XAM.java:178) at com.affymetrix.genometryImpl.symloader.BAM.parse(BAM.java:137) at com.affymetrix.genometryImpl.symloader.XAM.getRegion(XAM.java:122) at com.affymetrix.igb.featureloader.QuickLoad.getRegion(QuickLoad.java:402) at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:248) at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177) at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:906) at com.affymetrix.igb.view.load.GeneralLoadUtils.access$200(GeneralLoadUtils.java:88) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:839) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:834) at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) |
Windows v9967 IGB 1GB Pref -> Other options Activate 'Confirm before loading large data set' Local file 'DryCT2.sm.bam' (which is 1.8G) Do not adjust zoom Load data Did not confirm before loading and error thrown in console: Jan 25, 2012 4:05:25 PM com.affymetrix.igb.view.load.GeneralLoadUtils$2 finished SEVERE: Unable to get refresh action result. java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source) at java.util.concurrent.FutureTask.get(Unknown Source) at javax.swing.SwingWorker.get(Unknown Source) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:865) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.OutOfMemoryError: Java heap space at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:241) at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:229) at net.sf.samtools.SAMRecord.getBaseQualityString(SAMRecord.java:247) at com.affymetrix.genometryImpl.symloader.XAM.convertSAMRecordToSymWithProps(XAM.java:178) at com.affymetrix.genometryImpl.symloader.BAM.parse(BAM.java:137) at com.affymetrix.genometryImpl.symloader.XAM.getRegion(XAM.java:122) at com.affymetrix.igb.featureloader.QuickLoad.getRegion(QuickLoad.java:402) at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:248) at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177) at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:906) at com.affymetrix.igb.view.load.GeneralLoadUtils.access$200(GeneralLoadUtils.java:88) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:839) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:834) at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) |
| Description |
Windows v9967 IGB 1GB Pref -> Other options Activate 'Confirm before loading large data set' Local file 'DryCT2.sm.bam' (which is 1.8G) Do not adjust zoom Load data Did not confirm before loading and error thrown in console: Jan 25, 2012 4:05:25 PM com.affymetrix.igb.view.load.GeneralLoadUtils$2 finished SEVERE: Unable to get refresh action result. java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source) at java.util.concurrent.FutureTask.get(Unknown Source) at javax.swing.SwingWorker.get(Unknown Source) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:865) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.OutOfMemoryError: Java heap space at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:241) at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:229) at net.sf.samtools.SAMRecord.getBaseQualityString(SAMRecord.java:247) at com.affymetrix.genometryImpl.symloader.XAM.convertSAMRecordToSymWithProps(XAM.java:178) at com.affymetrix.genometryImpl.symloader.BAM.parse(BAM.java:137) at com.affymetrix.genometryImpl.symloader.XAM.getRegion(XAM.java:122) at com.affymetrix.igb.featureloader.QuickLoad.getRegion(QuickLoad.java:402) at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:248) at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177) at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:906) at com.affymetrix.igb.view.load.GeneralLoadUtils.access$200(GeneralLoadUtils.java:88) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:839) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:834) at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) |
Windows v9967 IGB 1GB Pref -> Other options Activate 'Confirm before loading large data set' Local file 'DryCT2.sm.bam' (which is 1.8G) Do not adjust zoom Load data Did not confirm before loading, file does not load, and error thrown in console: Jan 25, 2012 4:05:25 PM com.affymetrix.igb.view.load.GeneralLoadUtils$2 finished SEVERE: Unable to get refresh action result. java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source) at java.util.concurrent.FutureTask.get(Unknown Source) at javax.swing.SwingWorker.get(Unknown Source) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:865) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.OutOfMemoryError: Java heap space at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:241) at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:229) at net.sf.samtools.SAMRecord.getBaseQualityString(SAMRecord.java:247) at com.affymetrix.genometryImpl.symloader.XAM.convertSAMRecordToSymWithProps(XAM.java:178) at com.affymetrix.genometryImpl.symloader.BAM.parse(BAM.java:137) at com.affymetrix.genometryImpl.symloader.XAM.getRegion(XAM.java:122) at com.affymetrix.igb.featureloader.QuickLoad.getRegion(QuickLoad.java:402) at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:248) at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177) at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:906) at com.affymetrix.igb.view.load.GeneralLoadUtils.access$200(GeneralLoadUtils.java:88) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:839) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:834) at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) |
| Assignee | Ann Loraine [ aloraine ] | Alyssa Gulledge [ alyssa ] |
| Assignee | Alyssa Gulledge [ alyssa ] | Hiral Vora [ hiralv ] |
| Assignee | Hiral Vora [ hiralv ] | David Norris [ david ] |
| Assignee | David Norris [ david ] | Alyssa Gulledge [ alyssa ] |
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |