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  1. IGB 6.7
  2. IGBB-271

Did not 'Confirm before loading large data set' (Pref -> Other options)

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Fixed
    • 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

          Hide
          alyssa Alyssa Gulledge (Inactive) added a comment -

          On Mac, I also did not get the 'File too large' warning before trying to load the whole data set... please re-enable it!

          Show
          alyssa Alyssa Gulledge (Inactive) added a comment - On Mac, I also did not get the 'File too large' warning before trying to load the whole data set... please re-enable it!
          Hide
          hiralv Hiral Vora (Inactive) added a comment -

          Go ahead and remove this option. It's not used anymore.

          Show
          hiralv Hiral Vora (Inactive) added a comment - Go ahead and remove this option. It's not used anymore.
          Hide
          david David Norris (Inactive) added a comment -

          done in r10045

          Show
          david David Norris (Inactive) added a comment - done in r10045

            People

            • Assignee:
              Unassigned
              Reporter:
              kkubiak Katharine Kubiak (Inactive)
            • Votes:
              0 Vote for this issue
              Watchers:
              0 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: