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
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Environment:
Windows v9908
Description
1. Open IGB
2. No species loaded
3. Drag and drop in local .CHP file (attached)
Throws error in console:
MainWorkspaceManager:itemStateChanged hit
MainWorkspaceManager:itemStateChanged hit
Jan 23, 2012 1:24:05 PM com.affymetrix.igb.featureloader.QuickLoad logException
WARNING: BGZF file has invalid uncompressedLength: -216092498
java.lang.RuntimeException: BGZF file has invalid uncompressedLength: -216092498
at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:376)
at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361)
at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)
at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)
at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:159)
at com.affymetrix.genometryImpl.util.GeneralUtils.unzipFile(GeneralUtils.java:451)
at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:602)
at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:589)
at com.affymetrix.igb.featureloader.QuickLoad.getGenome(QuickLoad.java:379)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddAllSymmetries(QuickLoad.java:273)
at com.affymetrix.igb.featureloader.QuickLoad.access$000(QuickLoad.java:46)
at com.affymetrix.igb.featureloader.QuickLoad$1.runInBackground(QuickLoad.java:194)
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)
Caused by: java.lang.NegativeArraySizeException
at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:374)
... 19 more
Jan 23, 2012 1:24:05 PM com.affymetrix.igb.featureloader.QuickLoad logException
WARNING: null
java.lang.NullPointerException
at com.affymetrix.igb.featureloader.QuickLoad.addMethodsToFeature(QuickLoad.java:306)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddAllSymmetries(QuickLoad.java:286)
at com.affymetrix.igb.featureloader.QuickLoad.access$000(QuickLoad.java:46)
at com.affymetrix.igb.featureloader.QuickLoad$1.runInBackground(QuickLoad.java:194)
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)
MainWorkspaceManager:itemStateChanged hit
MainWorkspaceManager:itemStateChanged hit
Attachments
Issue Links
- relates to
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BUG-622 File format issues
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- Closed
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Activity
Still cannot reproduce.
well, then this is a weird error on my machine and I am going to put this bug to bed... 
Passed V.13624, Mac, Java 1.06.0_37 as the output is concurrent with an IMPROVEMENT discussed in the resolution of BUG-275
For Arabidopsis CHP file, 2 windows appear with the first being an Error stating:
-------------------------------------------------------
ERROR: Couldn't find genome data on server for file, genome = Unknown Genome 2
-------------------------------------------------------
and the second being an option from IGB to remove the file since it is not able to load.
The TisMap_Brain_01_v1_WTGene1.rma-gene-default.chp.gz caused IGB to react in the same manner with an error window and the option to remove the file since it is not able to load.
The Java console displayed the following errors:
net.sf.samtools.FileTruncatedException: Premature end of file
at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:359)
at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)
at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:275)
at java.io.BufferedInputStream.read(BufferedInputStream.java:334)
at java.io.FilterInputStream.read(FilterInputStream.java:107)
at com.affymetrix.genometryImpl.util.GeneralUtils.convertStreamToFile(GeneralUtils.java:189)
at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:645)
at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:606)
at com.affymetrix.igb.parsers.QuickLoadSymLoaderChp.getGenome(QuickLoadSymLoaderChp.java:66)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddAllSymmetries(QuickLoadSymLoader.java:158)
at com.affymetrix.igb.view.load.GeneralLoadUtils$5.runInBackground(GeneralLoadUtils.java:1414)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
Nov 28, 2012 3:39:17 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException
WARNING: null
java.lang.NullPointerException
at com.affymetrix.igb.parsers.QuickLoadSymLoaderChp.getGenome(QuickLoadSymLoaderChp.java:67)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddAllSymmetries(QuickLoadSymLoader.java:158)
at com.affymetrix.igb.view.load.GeneralLoadUtils$5.runInBackground(GeneralLoadUtils.java:1414)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
Nov 28, 2012 3:39:17 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException
WARNING: java.lang.NullPointerException
java.lang.RuntimeException: java.lang.NullPointerException
at com.affymetrix.igb.parsers.QuickLoadSymLoaderChp.getGenome(QuickLoadSymLoaderChp.java:72)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddAllSymmetries(QuickLoadSymLoader.java:158)
at com.affymetrix.igb.view.load.GeneralLoadUtils$5.runInBackground(GeneralLoadUtils.java:1414)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.NullPointerException
at com.affymetrix.igb.parsers.QuickLoadSymLoaderChp.getGenome(QuickLoadSymLoaderChp.java:67)
... 10 more
Hiral, this CHP used to work just fine. Has the CHP format been entirely set to 'legacy' status? Or is there a bug in the system?
CHP are genome specific and requires a active DAS2 server to load it properly.
Also, the file will show and be checked under 'Local Files' in the 'Data Access' tab, but when unchecking the file another error is thrown in the console:
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadAndDisplayAnnotations(GeneralLoadUtils.java:710)
at com.affymetrix.igb.view.load.GeneralLoadView.loadFeature(GeneralLoadView.java:315)
at com.affymetrix.igb.view.load.GeneralLoadView.addFeature(GeneralLoadView.java:575)
at com.affymetrix.igb.view.load.FeatureTreeView$FeatureTreeCellEditor$FeatureLoadAction.actionPerformed(FeatureTreeView.java:688)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.JToggleButton$ToggleButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at javax.swing.plaf.basic.BasicTreeUI$MouseInputHandler.mouseReleased(Unknown Source)
at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(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.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$2.run(Unknown Source)
at java.awt.EventQueue$2.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)